cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument#128

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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument #128

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cc93497
assure cbind gives unique colnames & barcodes are kept as colData
CATALYST-project Nov 17, 2022
8d81990
Update R-cmd-check.yaml
drighelli Nov 17, 2022
3ddd2c3
+withDimnames arg in spatialCoords getter&setter
CATALYST-project Nov 21, 2022
d8aabf6
add doc for param 'withDimnames'
CATALYST-project Nov 21, 2022
ac4bd0f
Merge branch 'cbind_unique_colnms' into spatialCoords
CATALYST-project Nov 21, 2022
1b4fad4
version bump to v1.9.4
CATALYST-project Nov 22, 2022
fe40c8f
fix bug in unit tests (uninitialized variable)
CATALYST-project Nov 22, 2022
2831903
resolve merge conflicts
CATALYST-project Nov 22, 2022
8842c22
update NEWS file v1.9.4
CATALYST-project Nov 24, 2022
fc2e6af
fix generic/method defintiions
CATALYST-project Nov 24, 2022
253e5e4
add doc for ... param
CATALYST-project Nov 24, 2022
0db2ad7
Merge branch 'devel' into cbind_unique_colnms
drighelli Sep 2, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments.
The class extends SingleCellExperiment to
The class extends SingleCellExperiment to
support storage and retrieval of additional information from spot-based and
molecule-based platforms, including spatial coordinates, images, and
image metadata. A specialized constructor function is included for data
Expand Down
2 changes: 1 addition & 1 deletion R/AllGenerics.R
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Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down
5 changes: 5 additions & 0 deletions R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R
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Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
out <- do.call(
callNextMethod,
c(args, list(deparse.level=1)))
if (any(duplicated(colnames(out)))) {
n <- vapply(args, ncol, integer(1))
n <- rep.int(seq_along(args), n)
colnames(out) <- paste(n, colnames(out), sep="_")
}

# merge 'imgData' from multiple samples
if (!is.null(imgData(args[[1]]))) {
Expand Down
70 changes: 7 additions & 63 deletions R/SpatialExperiment-methods.R
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Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)}
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#'
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
}
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords",
"SpatialExperiment",
function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords",
c("SpatialExperiment", "matrix"),
function(x, value) {
stopifnot(
is.numeric(value),
nrow(value) == ncol(x))
int_colData(x)$spatialCoords <- value
return(x)
}
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords",
c("SpatialExperiment", "NULL"),
function(x, value) {
value <- matrix(numeric(), ncol(x), 0)
`spatialCoords<-`(x, value)
}
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames",
"SpatialExperiment",
function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames",
c("SpatialExperiment", "character"),
function(x, value) {
colnames(int_colData(x)$spatialCoords) <- value
return(x)
}
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames",
c("SpatialExperiment", "NULL"),
function(x, value) {
value <- character()
`spatialCoordsNames<-`(x, value)
}
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down
8 changes: 3 additions & 5 deletions R/read10xVisium.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
cnms <- c(
"barcode", "in_tissue", "array_row", "array_col",
"pxl_row_in_fullres", "pxl_col_in_fullres")
df <- lapply(seq_along(x), function(i)
{
df <- read.csv(x[i],
header=!grepl("list", x[i]),
row.names=1, col.names=cnms)
df <- lapply(seq_along(x), function(i) {
df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
rownames(df) <- df$barcode
df
})
df <- do.call(rbind, df)
Expand Down
77 changes: 77 additions & 0 deletions R/spatialCoords.R
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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords",
"SpatialExperiment",
function(x, withDimnames=TRUE, ...) {
out <- int_colData(x)$spatialCoords
if (withDimnames)
rownames(out) <- colnames(x)
return(out)
})

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords",
c("SpatialExperiment", "matrix"),

@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"

Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…

@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?

@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))

@HelenaLCHelenaLCNov 22, 2022•
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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…

@drighellidrighelliNov 23, 2022

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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.

function(x, withDimnames=TRUE, ..., value) {
stopifnot(
is.numeric(value),
nrow(value) == ncol(x))
new <- rownames(value)
if (!is.null(new) && withDimnames) {
if (!identical(new, colnames(x))) {
stop("Non-NULL 'rownames(value)' should be the",
" same as 'colnames(x)' for 'spatialCoords<-'.",
" Use 'withDimnames=FALSE' to force replacement.")
}
}
int_colData(x)$spatialCoords <- value
return(x)
}
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords",
c("SpatialExperiment", "NULL"),
function(x, withDimnames=TRUE, ..., value) {
`spatialCoords<-`(x,
withDimnames=withDimnames, ...,
value=matrix(numeric(), ncol(x), 0))
}
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames",
"SpatialExperiment",
function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames",
c("SpatialExperiment", "character"),
function(x, value) {
colnames(int_colData(x)$spatialCoords) <- value
return(x)
}
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames",
c("SpatialExperiment", "NULL"),
function(x, value) {
value <- character()
`spatialCoordsNames<-`(x, value)
}
)
6 changes: 6 additions & 0 deletions inst/NEWS
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Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in
datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
(analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

Expand Down
2 changes: 1 addition & 1 deletion man/SpatialExperiment-combine.Rd
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44 changes: 27 additions & 17 deletions man/SpatialExperiment-methods.Rd
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13 changes: 12 additions & 1 deletion tests/testthat/test_SpatialExperiment-cbind.R
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Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
expect_true(nrow(new) == nrow(spe))
expect_true(ncol(new) == 2*ncol(spe))
expect_identical(rownames(new), rownames(spe))
expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
expect_identical(imgData(spe3)[one, ], imgData(spe1))
expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
tmp <- spe
colnames(tmp) <- paste0(colnames(tmp), "x")
out <- cbind(spe, tmp)
expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
out <- cbind(spe, spe)
expect_false(any(duplicated(colnames(out))))
})
22 changes: 0 additions & 22 deletions tests/testthat/test_SpatialExperiment-methods.R
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Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
expect_identical(
spatialCoordsNames(spe),
colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
old <- spatialCoordsNames(spe)
new <- sample(letters, length(old))
spatialCoordsNames(spe) <- new
expect_identical(spatialCoordsNames(spe), new)
expect_identical(spatialCoordsNames(spe),
colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
old <- spatialCoords(spe)
spatialCoordsNames(spe) <- NULL
expect_null(spatialCoordsNames(spe))
expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
expect_is(sfs, "numeric")
Expand Down
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument#128

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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument
#128
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cc93497

assure cbind gives unique colnames & barcodes are kept as colData


CATALYST-project Nov 17, 2022
8d81990

Update R-cmd-check.yaml


drighelli Nov 17, 2022
3ddd2c3

+withDimnames arg in spatialCoords getter&setter


CATALYST-project Nov 21, 2022
d8aabf6

add doc for param 'withDimnames'


CATALYST-project Nov 21, 2022
ac4bd0f

Merge branch 'cbind_unique_colnms' into spatialCoords


CATALYST-project Nov 21, 2022
1b4fad4

version bump to v1.9.4


CATALYST-project Nov 22, 2022
fe40c8f

fix bug in unit tests (uninitialized variable)


CATALYST-project Nov 22, 2022
2831903

resolve merge conflicts


CATALYST-project Nov 22, 2022
8842c22

update NEWS file v1.9.4


CATALYST-project Nov 24, 2022
fc2e6af

fix generic/method defintiions


CATALYST-project Nov 24, 2022
253e5e4

add doc for ... param


CATALYST-project Nov 24, 2022
0db2ad7

Merge branch 'devel' into cbind_unique_colnms


drighelli Sep 2, 2023

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2 changes: 1 addition & 1 deletion
DESCRIPTION

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments. 
 The class extends SingleCellExperiment to
 The class extends SingleCellExperiment to
 support storage and retrieval of additional information from spot-based and 
 molecule-based platforms, including spatial coordinates, images, and 
 image metadata. A specialized constructor function is included for data 
Expand Down

2 changes: 1 addition & 1 deletion
R/AllGenerics.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down

5 changes: 5 additions & 0 deletions
R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
 out <- do.call(
 callNextMethod, 
 c(args, list(deparse.level=1)))
 if (any(duplicated(colnames(out)))) {
 n <- vapply(args, ncol, integer(1))
 n <- rep.int(seq_along(args), n)
 colnames(out) <- paste(n, colnames(out), sep="_")
 }

 # merge 'imgData' from multiple samples
 if (!is.null(imgData(args[[1]]))) { 
Expand Down

70 changes: 7 additions & 63 deletions
R/SpatialExperiment-methods.R

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Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)} 
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#' 
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
 }
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
 function(x, value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, value) {
 value <- matrix(numeric(), ncol(x), 0)
 `spatialCoords<-`(x, value)
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down

8 changes: 3 additions & 5 deletions
R/read10xVisium.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
 cnms <- c(
 "barcode", "in_tissue", "array_row", "array_col", 
 "pxl_row_in_fullres", "pxl_col_in_fullres")
 df <- lapply(seq_along(x), function(i) 
 {
 df <- read.csv(x[i], 
 header=!grepl("list", x[i]), 
 row.names=1, col.names=cnms)
 df <- lapply(seq_along(x), function(i) {
 df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
 if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
 if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
 rownames(df) <- df$barcode
 df
 })
 df <- do.call(rbind, df)
Expand Down

77 changes: 77 additions & 0 deletions
R/spatialCoords.R

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x, withDimnames=TRUE, ...) {
 out <- int_colData(x)$spatialCoords
 if (withDimnames) 
 rownames(out) <- colnames(x)
 return(out)
 })

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"
Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…
@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?
@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))
@HelenaLCHelenaLCNov 22, 2022•

edited

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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…
@drighellidrighelliNov 23, 2022

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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.
 function(x, withDimnames=TRUE, ..., value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 new <- rownames(value)
 if (!is.null(new) && withDimnames) {
 if (!identical(new, colnames(x))) {
 stop("Non-NULL 'rownames(value)' should be the",
 " same as 'colnames(x)' for 'spatialCoords<-'.",
 " Use 'withDimnames=FALSE' to force replacement.")
 }
 }
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, withDimnames=TRUE, ..., value) {
 `spatialCoords<-`(x, 
 withDimnames=withDimnames, ..., 
 value=matrix(numeric(), ncol(x), 0))
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

6 changes: 6 additions & 0 deletions
inst/NEWS

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in 
 datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
 (analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

Expand Down

2 changes: 1 addition & 1 deletion
man/SpatialExperiment-combine.Rd

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44 changes: 27 additions & 17 deletions
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13 changes: 12 additions & 1 deletion
tests/testthat/test_SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
 expect_true(nrow(new) == nrow(spe))
 expect_true(ncol(new) == 2*ncol(spe))
 expect_identical(rownames(new), rownames(spe))
 expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
 expect_identical(imgData(spe3)[one, ], imgData(spe1))
 expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
 tmp <- spe
 colnames(tmp) <- paste0(colnames(tmp), "x")
 out <- cbind(spe, tmp)
 expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
 out <- cbind(spe, spe)
 expect_false(any(duplicated(colnames(out))))
})

22 changes: 0 additions & 22 deletions
tests/testthat/test_SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
 expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
 expect_identical(
 spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
 old <- spatialCoordsNames(spe)
 new <- sample(letters, length(old))
 spatialCoordsNames(spe) <- new
 expect_identical(spatialCoordsNames(spe), new)
 expect_identical(spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
 old <- spatialCoords(spe)
 spatialCoordsNames(spe) <- NULL
 expect_null(spatialCoordsNames(spe))
 expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
 sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
 expect_is(sfs, "numeric")
Expand Down
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument#128

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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument
#128
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cc93497

assure cbind gives unique colnames & barcodes are kept as colData


CATALYST-project Nov 17, 2022
8d81990

Update R-cmd-check.yaml


drighelli Nov 17, 2022
3ddd2c3

+withDimnames arg in spatialCoords getter&setter


CATALYST-project Nov 21, 2022
d8aabf6

add doc for param 'withDimnames'


CATALYST-project Nov 21, 2022
ac4bd0f

Merge branch 'cbind_unique_colnms' into spatialCoords


CATALYST-project Nov 21, 2022
1b4fad4

version bump to v1.9.4


CATALYST-project Nov 22, 2022
fe40c8f

fix bug in unit tests (uninitialized variable)


CATALYST-project Nov 22, 2022
2831903

resolve merge conflicts


CATALYST-project Nov 22, 2022
8842c22

update NEWS file v1.9.4


CATALYST-project Nov 24, 2022
fc2e6af

fix generic/method defintiions


CATALYST-project Nov 24, 2022
253e5e4

add doc for ... param


CATALYST-project Nov 24, 2022
0db2ad7

Merge branch 'devel' into cbind_unique_colnms


drighelli Sep 2, 2023

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2 changes: 1 addition & 1 deletion
DESCRIPTION

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments. 
 The class extends SingleCellExperiment to
 The class extends SingleCellExperiment to
 support storage and retrieval of additional information from spot-based and 
 molecule-based platforms, including spatial coordinates, images, and 
 image metadata. A specialized constructor function is included for data 
Expand Down

2 changes: 1 addition & 1 deletion
R/AllGenerics.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down

5 changes: 5 additions & 0 deletions
R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
 out <- do.call(
 callNextMethod, 
 c(args, list(deparse.level=1)))
 if (any(duplicated(colnames(out)))) {
 n <- vapply(args, ncol, integer(1))
 n <- rep.int(seq_along(args), n)
 colnames(out) <- paste(n, colnames(out), sep="_")
 }

 # merge 'imgData' from multiple samples
 if (!is.null(imgData(args[[1]]))) { 
Expand Down

70 changes: 7 additions & 63 deletions
R/SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)} 
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#' 
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
 }
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
 function(x, value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, value) {
 value <- matrix(numeric(), ncol(x), 0)
 `spatialCoords<-`(x, value)
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down

8 changes: 3 additions & 5 deletions
R/read10xVisium.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
 cnms <- c(
 "barcode", "in_tissue", "array_row", "array_col", 
 "pxl_row_in_fullres", "pxl_col_in_fullres")
 df <- lapply(seq_along(x), function(i) 
 {
 df <- read.csv(x[i], 
 header=!grepl("list", x[i]), 
 row.names=1, col.names=cnms)
 df <- lapply(seq_along(x), function(i) {
 df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
 if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
 if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
 rownames(df) <- df$barcode
 df
 })
 df <- do.call(rbind, df)
Expand Down

77 changes: 77 additions & 0 deletions
R/spatialCoords.R

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x, withDimnames=TRUE, ...) {
 out <- int_colData(x)$spatialCoords
 if (withDimnames) 
 rownames(out) <- colnames(x)
 return(out)
 })

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"
Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…
@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?
@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))
@HelenaLCHelenaLCNov 22, 2022•

edited

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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…
@drighellidrighelliNov 23, 2022

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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.
 function(x, withDimnames=TRUE, ..., value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 new <- rownames(value)
 if (!is.null(new) && withDimnames) {
 if (!identical(new, colnames(x))) {
 stop("Non-NULL 'rownames(value)' should be the",
 " same as 'colnames(x)' for 'spatialCoords<-'.",
 " Use 'withDimnames=FALSE' to force replacement.")
 }
 }
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, withDimnames=TRUE, ..., value) {
 `spatialCoords<-`(x, 
 withDimnames=withDimnames, ..., 
 value=matrix(numeric(), ncol(x), 0))
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

6 changes: 6 additions & 0 deletions
inst/NEWS

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in 
 datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
 (analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

Expand Down

2 changes: 1 addition & 1 deletion
man/SpatialExperiment-combine.Rd

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man/SpatialExperiment-methods.Rd

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13 changes: 12 additions & 1 deletion
tests/testthat/test_SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
 expect_true(nrow(new) == nrow(spe))
 expect_true(ncol(new) == 2*ncol(spe))
 expect_identical(rownames(new), rownames(spe))
 expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
 expect_identical(imgData(spe3)[one, ], imgData(spe1))
 expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
 tmp <- spe
 colnames(tmp) <- paste0(colnames(tmp), "x")
 out <- cbind(spe, tmp)
 expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
 out <- cbind(spe, spe)
 expect_false(any(duplicated(colnames(out))))
})

22 changes: 0 additions & 22 deletions
tests/testthat/test_SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
 expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
 expect_identical(
 spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
 old <- spatialCoordsNames(spe)
 new <- sample(letters, length(old))
 spatialCoordsNames(spe) <- new
 expect_identical(spatialCoordsNames(spe), new)
 expect_identical(spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
 old <- spatialCoords(spe)
 spatialCoordsNames(spe) <- NULL
 expect_null(spatialCoordsNames(spe))
 expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
 sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
 expect_is(sfs, "numeric")
Expand Down
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument#128

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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument
#128
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cc93497

assure cbind gives unique colnames & barcodes are kept as colData


CATALYST-project Nov 17, 2022
8d81990

Update R-cmd-check.yaml


drighelli Nov 17, 2022
3ddd2c3

+withDimnames arg in spatialCoords getter&setter


CATALYST-project Nov 21, 2022
d8aabf6

add doc for param 'withDimnames'


CATALYST-project Nov 21, 2022
ac4bd0f

Merge branch 'cbind_unique_colnms' into spatialCoords


CATALYST-project Nov 21, 2022
1b4fad4

version bump to v1.9.4


CATALYST-project Nov 22, 2022
fe40c8f

fix bug in unit tests (uninitialized variable)


CATALYST-project Nov 22, 2022
2831903

resolve merge conflicts


CATALYST-project Nov 22, 2022
8842c22

update NEWS file v1.9.4


CATALYST-project Nov 24, 2022
fc2e6af

fix generic/method defintiions


CATALYST-project Nov 24, 2022
253e5e4

add doc for ... param


CATALYST-project Nov 24, 2022
0db2ad7

Merge branch 'devel' into cbind_unique_colnms


drighelli Sep 2, 2023

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2 changes: 1 addition & 1 deletion
DESCRIPTION

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments. 
 The class extends SingleCellExperiment to
 The class extends SingleCellExperiment to
 support storage and retrieval of additional information from spot-based and 
 molecule-based platforms, including spatial coordinates, images, and 
 image metadata. A specialized constructor function is included for data 
Expand Down

2 changes: 1 addition & 1 deletion
R/AllGenerics.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down

5 changes: 5 additions & 0 deletions
R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
 out <- do.call(
 callNextMethod, 
 c(args, list(deparse.level=1)))
 if (any(duplicated(colnames(out)))) {
 n <- vapply(args, ncol, integer(1))
 n <- rep.int(seq_along(args), n)
 colnames(out) <- paste(n, colnames(out), sep="_")
 }

 # merge 'imgData' from multiple samples
 if (!is.null(imgData(args[[1]]))) { 
Expand Down

70 changes: 7 additions & 63 deletions
R/SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)} 
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#' 
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
 }
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
 function(x, value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, value) {
 value <- matrix(numeric(), ncol(x), 0)
 `spatialCoords<-`(x, value)
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down

8 changes: 3 additions & 5 deletions
R/read10xVisium.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
 cnms <- c(
 "barcode", "in_tissue", "array_row", "array_col", 
 "pxl_row_in_fullres", "pxl_col_in_fullres")
 df <- lapply(seq_along(x), function(i) 
 {
 df <- read.csv(x[i], 
 header=!grepl("list", x[i]), 
 row.names=1, col.names=cnms)
 df <- lapply(seq_along(x), function(i) {
 df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
 if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
 if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
 rownames(df) <- df$barcode
 df
 })
 df <- do.call(rbind, df)
Expand Down

77 changes: 77 additions & 0 deletions
R/spatialCoords.R

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x, withDimnames=TRUE, ...) {
 out <- int_colData(x)$spatialCoords
 if (withDimnames) 
 rownames(out) <- colnames(x)
 return(out)
 })

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"
Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…
@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?
@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))
@HelenaLCHelenaLCNov 22, 2022•

edited

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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…
@drighellidrighelliNov 23, 2022

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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.
 function(x, withDimnames=TRUE, ..., value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 new <- rownames(value)
 if (!is.null(new) && withDimnames) {
 if (!identical(new, colnames(x))) {
 stop("Non-NULL 'rownames(value)' should be the",
 " same as 'colnames(x)' for 'spatialCoords<-'.",
 " Use 'withDimnames=FALSE' to force replacement.")
 }
 }
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, withDimnames=TRUE, ..., value) {
 `spatialCoords<-`(x, 
 withDimnames=withDimnames, ..., 
 value=matrix(numeric(), ncol(x), 0))
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

6 changes: 6 additions & 0 deletions
inst/NEWS

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in 
 datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
 (analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

Expand Down

2 changes: 1 addition & 1 deletion
man/SpatialExperiment-combine.Rd

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44 changes: 27 additions & 17 deletions
man/SpatialExperiment-methods.Rd

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13 changes: 12 additions & 1 deletion
tests/testthat/test_SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
 expect_true(nrow(new) == nrow(spe))
 expect_true(ncol(new) == 2*ncol(spe))
 expect_identical(rownames(new), rownames(spe))
 expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
 expect_identical(imgData(spe3)[one, ], imgData(spe1))
 expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
 tmp <- spe
 colnames(tmp) <- paste0(colnames(tmp), "x")
 out <- cbind(spe, tmp)
 expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
 out <- cbind(spe, spe)
 expect_false(any(duplicated(colnames(out))))
})

22 changes: 0 additions & 22 deletions
tests/testthat/test_SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
 expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
 expect_identical(
 spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
 old <- spatialCoordsNames(spe)
 new <- sample(letters, length(old))
 spatialCoordsNames(spe) <- new
 expect_identical(spatialCoordsNames(spe), new)
 expect_identical(spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
 old <- spatialCoords(spe)
 spatialCoordsNames(spe) <- NULL
 expect_null(spatialCoordsNames(spe))
 expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
 sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
 expect_is(sfs, "numeric")
Expand Down
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if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
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return changed ? u.toString() : url;
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function cleanLinks() {
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var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
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} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument#128

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HelenaLC
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12
commits into

base:devel
Choose a base branch

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 Open

cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument
#128
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cc93497

assure cbind gives unique colnames & barcodes are kept as colData


CATALYST-project Nov 17, 2022
8d81990

Update R-cmd-check.yaml


drighelli Nov 17, 2022
3ddd2c3

+withDimnames arg in spatialCoords getter&setter


CATALYST-project Nov 21, 2022
d8aabf6

add doc for param 'withDimnames'


CATALYST-project Nov 21, 2022
ac4bd0f

Merge branch 'cbind_unique_colnms' into spatialCoords


CATALYST-project Nov 21, 2022
1b4fad4

version bump to v1.9.4


CATALYST-project Nov 22, 2022
fe40c8f

fix bug in unit tests (uninitialized variable)


CATALYST-project Nov 22, 2022
2831903

resolve merge conflicts


CATALYST-project Nov 22, 2022
8842c22

update NEWS file v1.9.4


CATALYST-project Nov 24, 2022
fc2e6af

fix generic/method defintiions


CATALYST-project Nov 24, 2022
253e5e4

add doc for ... param


CATALYST-project Nov 24, 2022
0db2ad7

Merge branch 'devel' into cbind_unique_colnms


drighelli Sep 2, 2023

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2 changes: 1 addition & 1 deletion
DESCRIPTION

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments. 
 The class extends SingleCellExperiment to
 The class extends SingleCellExperiment to
 support storage and retrieval of additional information from spot-based and 
 molecule-based platforms, including spatial coordinates, images, and 
 image metadata. A specialized constructor function is included for data 
Expand Down

2 changes: 1 addition & 1 deletion
R/AllGenerics.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down

5 changes: 5 additions & 0 deletions
R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
 out <- do.call(
 callNextMethod, 
 c(args, list(deparse.level=1)))
 if (any(duplicated(colnames(out)))) {
 n <- vapply(args, ncol, integer(1))
 n <- rep.int(seq_along(args), n)
 colnames(out) <- paste(n, colnames(out), sep="_")
 }

 # merge 'imgData' from multiple samples
 if (!is.null(imgData(args[[1]]))) { 
Expand Down

70 changes: 7 additions & 63 deletions
R/SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)} 
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#' 
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
 }
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
 function(x, value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, value) {
 value <- matrix(numeric(), ncol(x), 0)
 `spatialCoords<-`(x, value)
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down

8 changes: 3 additions & 5 deletions
R/read10xVisium.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
 cnms <- c(
 "barcode", "in_tissue", "array_row", "array_col", 
 "pxl_row_in_fullres", "pxl_col_in_fullres")
 df <- lapply(seq_along(x), function(i) 
 {
 df <- read.csv(x[i], 
 header=!grepl("list", x[i]), 
 row.names=1, col.names=cnms)
 df <- lapply(seq_along(x), function(i) {
 df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
 if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
 if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
 rownames(df) <- df$barcode
 df
 })
 df <- do.call(rbind, df)
Expand Down

77 changes: 77 additions & 0 deletions
R/spatialCoords.R

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x, withDimnames=TRUE, ...) {
 out <- int_colData(x)$spatialCoords
 if (withDimnames) 
 rownames(out) <- colnames(x)
 return(out)
 })

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"
Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…
@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?
@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))
@HelenaLCHelenaLCNov 22, 2022•

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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…
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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.
 function(x, withDimnames=TRUE, ..., value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 new <- rownames(value)
 if (!is.null(new) && withDimnames) {
 if (!identical(new, colnames(x))) {
 stop("Non-NULL 'rownames(value)' should be the",
 " same as 'colnames(x)' for 'spatialCoords<-'.",
 " Use 'withDimnames=FALSE' to force replacement.")
 }
 }
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, withDimnames=TRUE, ..., value) {
 `spatialCoords<-`(x, 
 withDimnames=withDimnames, ..., 
 value=matrix(numeric(), ncol(x), 0))
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

6 changes: 6 additions & 0 deletions
inst/NEWS

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in 
 datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
 (analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

Expand Down

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tests/testthat/test_SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
 expect_true(nrow(new) == nrow(spe))
 expect_true(ncol(new) == 2*ncol(spe))
 expect_identical(rownames(new), rownames(spe))
 expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
 expect_identical(imgData(spe3)[one, ], imgData(spe1))
 expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
 tmp <- spe
 colnames(tmp) <- paste0(colnames(tmp), "x")
 out <- cbind(spe, tmp)
 expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
 out <- cbind(spe, spe)
 expect_false(any(duplicated(colnames(out))))
})

22 changes: 0 additions & 22 deletions
tests/testthat/test_SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
 expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
 expect_identical(
 spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
 old <- spatialCoordsNames(spe)
 new <- sample(letters, length(old))
 spatialCoordsNames(spe) <- new
 expect_identical(spatialCoordsNames(spe), new)
 expect_identical(spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
 old <- spatialCoords(spe)
 spatialCoordsNames(spe) <- NULL
 expect_null(spatialCoordsNames(spe))
 expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
 sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
 expect_is(sfs, "numeric")
Expand Down
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument#128

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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument
#128
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cc93497

assure cbind gives unique colnames & barcodes are kept as colData


CATALYST-project Nov 17, 2022
8d81990

Update R-cmd-check.yaml


drighelli Nov 17, 2022
3ddd2c3

+withDimnames arg in spatialCoords getter&setter


CATALYST-project Nov 21, 2022
d8aabf6

add doc for param 'withDimnames'


CATALYST-project Nov 21, 2022
ac4bd0f

Merge branch 'cbind_unique_colnms' into spatialCoords


CATALYST-project Nov 21, 2022
1b4fad4

version bump to v1.9.4


CATALYST-project Nov 22, 2022
fe40c8f

fix bug in unit tests (uninitialized variable)


CATALYST-project Nov 22, 2022
2831903

resolve merge conflicts


CATALYST-project Nov 22, 2022
8842c22

update NEWS file v1.9.4


CATALYST-project Nov 24, 2022
fc2e6af

fix generic/method defintiions


CATALYST-project Nov 24, 2022
253e5e4

add doc for ... param


CATALYST-project Nov 24, 2022
0db2ad7

Merge branch 'devel' into cbind_unique_colnms


drighelli Sep 2, 2023

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2 changes: 1 addition & 1 deletion
DESCRIPTION

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Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments. 
 The class extends SingleCellExperiment to
 The class extends SingleCellExperiment to
 support storage and retrieval of additional information from spot-based and 
 molecule-based platforms, including spatial coordinates, images, and 
 image metadata. A specialized constructor function is included for data 
Expand Down

2 changes: 1 addition & 1 deletion
R/AllGenerics.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down

5 changes: 5 additions & 0 deletions
R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
 out <- do.call(
 callNextMethod, 
 c(args, list(deparse.level=1)))
 if (any(duplicated(colnames(out)))) {
 n <- vapply(args, ncol, integer(1))
 n <- rep.int(seq_along(args), n)
 colnames(out) <- paste(n, colnames(out), sep="_")
 }

 # merge 'imgData' from multiple samples
 if (!is.null(imgData(args[[1]]))) { 
Expand Down

70 changes: 7 additions & 63 deletions
R/SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)} 
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#' 
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
 }
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
 function(x, value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, value) {
 value <- matrix(numeric(), ncol(x), 0)
 `spatialCoords<-`(x, value)
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down

8 changes: 3 additions & 5 deletions
R/read10xVisium.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
 cnms <- c(
 "barcode", "in_tissue", "array_row", "array_col", 
 "pxl_row_in_fullres", "pxl_col_in_fullres")
 df <- lapply(seq_along(x), function(i) 
 {
 df <- read.csv(x[i], 
 header=!grepl("list", x[i]), 
 row.names=1, col.names=cnms)
 df <- lapply(seq_along(x), function(i) {
 df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
 if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
 if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
 rownames(df) <- df$barcode
 df
 })
 df <- do.call(rbind, df)
Expand Down

77 changes: 77 additions & 0 deletions
R/spatialCoords.R

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x, withDimnames=TRUE, ...) {
 out <- int_colData(x)$spatialCoords
 if (withDimnames) 
 rownames(out) <- colnames(x)
 return(out)
 })

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"
Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…
@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?
@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))
@HelenaLCHelenaLCNov 22, 2022•

edited

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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…
@drighellidrighelliNov 23, 2022

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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.
 function(x, withDimnames=TRUE, ..., value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 new <- rownames(value)
 if (!is.null(new) && withDimnames) {
 if (!identical(new, colnames(x))) {
 stop("Non-NULL 'rownames(value)' should be the",
 " same as 'colnames(x)' for 'spatialCoords<-'.",
 " Use 'withDimnames=FALSE' to force replacement.")
 }
 }
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, withDimnames=TRUE, ..., value) {
 `spatialCoords<-`(x, 
 withDimnames=withDimnames, ..., 
 value=matrix(numeric(), ncol(x), 0))
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

6 changes: 6 additions & 0 deletions
inst/NEWS

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in 
 datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
 (analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

Expand Down

2 changes: 1 addition & 1 deletion
man/SpatialExperiment-combine.Rd

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13 changes: 12 additions & 1 deletion
tests/testthat/test_SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
 expect_true(nrow(new) == nrow(spe))
 expect_true(ncol(new) == 2*ncol(spe))
 expect_identical(rownames(new), rownames(spe))
 expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
 expect_identical(imgData(spe3)[one, ], imgData(spe1))
 expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
 tmp <- spe
 colnames(tmp) <- paste0(colnames(tmp), "x")
 out <- cbind(spe, tmp)
 expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
 out <- cbind(spe, spe)
 expect_false(any(duplicated(colnames(out))))
})

22 changes: 0 additions & 22 deletions
tests/testthat/test_SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
 expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
 expect_identical(
 spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
 old <- spatialCoordsNames(spe)
 new <- sample(letters, length(old))
 spatialCoordsNames(spe) <- new
 expect_identical(spatialCoordsNames(spe), new)
 expect_identical(spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
 old <- spatialCoords(spe)
 spatialCoordsNames(spe) <- NULL
 expect_null(spatialCoordsNames(spe))
 expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
 sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
 expect_is(sfs, "numeric")
Expand Down
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument#128

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HelenaLC
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument
#128
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cc93497

assure cbind gives unique colnames & barcodes are kept as colData


CATALYST-project Nov 17, 2022
8d81990

Update R-cmd-check.yaml


drighelli Nov 17, 2022
3ddd2c3

+withDimnames arg in spatialCoords getter&setter


CATALYST-project Nov 21, 2022
d8aabf6

add doc for param 'withDimnames'


CATALYST-project Nov 21, 2022
ac4bd0f

Merge branch 'cbind_unique_colnms' into spatialCoords


CATALYST-project Nov 21, 2022
1b4fad4

version bump to v1.9.4


CATALYST-project Nov 22, 2022
fe40c8f

fix bug in unit tests (uninitialized variable)


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2831903

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8842c22

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CATALYST-project Nov 24, 2022
fc2e6af

fix generic/method defintiions


CATALYST-project Nov 24, 2022
253e5e4

add doc for ... param


CATALYST-project Nov 24, 2022
0db2ad7

Merge branch 'devel' into cbind_unique_colnms


drighelli Sep 2, 2023

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2 changes: 1 addition & 1 deletion
DESCRIPTION

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments. 
 The class extends SingleCellExperiment to
 The class extends SingleCellExperiment to
 support storage and retrieval of additional information from spot-based and 
 molecule-based platforms, including spatial coordinates, images, and 
 image metadata. A specialized constructor function is included for data 
Expand Down

2 changes: 1 addition & 1 deletion
R/AllGenerics.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down

5 changes: 5 additions & 0 deletions
R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
 out <- do.call(
 callNextMethod, 
 c(args, list(deparse.level=1)))
 if (any(duplicated(colnames(out)))) {
 n <- vapply(args, ncol, integer(1))
 n <- rep.int(seq_along(args), n)
 colnames(out) <- paste(n, colnames(out), sep="_")
 }

 # merge 'imgData' from multiple samples
 if (!is.null(imgData(args[[1]]))) { 
Expand Down

70 changes: 7 additions & 63 deletions
R/SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)} 
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#' 
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
 }
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
 function(x, value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, value) {
 value <- matrix(numeric(), ncol(x), 0)
 `spatialCoords<-`(x, value)
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down

8 changes: 3 additions & 5 deletions
R/read10xVisium.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
 cnms <- c(
 "barcode", "in_tissue", "array_row", "array_col", 
 "pxl_row_in_fullres", "pxl_col_in_fullres")
 df <- lapply(seq_along(x), function(i) 
 {
 df <- read.csv(x[i], 
 header=!grepl("list", x[i]), 
 row.names=1, col.names=cnms)
 df <- lapply(seq_along(x), function(i) {
 df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
 if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
 if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
 rownames(df) <- df$barcode
 df
 })
 df <- do.call(rbind, df)
Expand Down

77 changes: 77 additions & 0 deletions
R/spatialCoords.R

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x, withDimnames=TRUE, ...) {
 out <- int_colData(x)$spatialCoords
 if (withDimnames) 
 rownames(out) <- colnames(x)
 return(out)
 })

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"
Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…
@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?
@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))
@HelenaLCHelenaLCNov 22, 2022•

edited

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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…
@drighellidrighelliNov 23, 2022

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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.
 function(x, withDimnames=TRUE, ..., value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 new <- rownames(value)
 if (!is.null(new) && withDimnames) {
 if (!identical(new, colnames(x))) {
 stop("Non-NULL 'rownames(value)' should be the",
 " same as 'colnames(x)' for 'spatialCoords<-'.",
 " Use 'withDimnames=FALSE' to force replacement.")
 }
 }
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, withDimnames=TRUE, ..., value) {
 `spatialCoords<-`(x, 
 withDimnames=withDimnames, ..., 
 value=matrix(numeric(), ncol(x), 0))
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

6 changes: 6 additions & 0 deletions
inst/NEWS

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in 
 datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
 (analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

Expand Down

2 changes: 1 addition & 1 deletion
man/SpatialExperiment-combine.Rd

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44 changes: 27 additions & 17 deletions
man/SpatialExperiment-methods.Rd

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13 changes: 12 additions & 1 deletion
tests/testthat/test_SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
 expect_true(nrow(new) == nrow(spe))
 expect_true(ncol(new) == 2*ncol(spe))
 expect_identical(rownames(new), rownames(spe))
 expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
 expect_identical(imgData(spe3)[one, ], imgData(spe1))
 expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
 tmp <- spe
 colnames(tmp) <- paste0(colnames(tmp), "x")
 out <- cbind(spe, tmp)
 expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
 out <- cbind(spe, spe)
 expect_false(any(duplicated(colnames(out))))
})

22 changes: 0 additions & 22 deletions
tests/testthat/test_SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
 expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
 expect_identical(
 spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
 old <- spatialCoordsNames(spe)
 new <- sample(letters, length(old))
 spatialCoordsNames(spe) <- new
 expect_identical(spatialCoordsNames(spe), new)
 expect_identical(spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
 old <- spatialCoords(spe)
 spatialCoordsNames(spe) <- NULL
 expect_null(spatialCoordsNames(spe))
 expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
 sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
 expect_is(sfs, "numeric")
Expand Down
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cbind: unique/duplicated colnamesare left asis/made unique; read10xVisium: keep barcodes as colData; spatialCoords/<-: withDimnames argument
#128
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cc93497

assure cbind gives unique colnames & barcodes are kept as colData


CATALYST-project Nov 17, 2022
8d81990

Update R-cmd-check.yaml


drighelli Nov 17, 2022
3ddd2c3

+withDimnames arg in spatialCoords getter&setter


CATALYST-project Nov 21, 2022
d8aabf6

add doc for param 'withDimnames'


CATALYST-project Nov 21, 2022
ac4bd0f

Merge branch 'cbind_unique_colnms' into spatialCoords


CATALYST-project Nov 21, 2022
1b4fad4

version bump to v1.9.4


CATALYST-project Nov 22, 2022
fe40c8f

fix bug in unit tests (uninitialized variable)


CATALYST-project Nov 22, 2022
2831903

resolve merge conflicts


CATALYST-project Nov 22, 2022
8842c22

update NEWS file v1.9.4


CATALYST-project Nov 24, 2022
fc2e6af

fix generic/method defintiions


CATALYST-project Nov 24, 2022
253e5e4

add doc for ... param


CATALYST-project Nov 24, 2022
0db2ad7

Merge branch 'devel' into cbind_unique_colnms


drighelli Sep 2, 2023

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2 changes: 1 addition & 1 deletion
DESCRIPTION

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,7 +2,7 @@ Package: SpatialExperiment
Version: 1.11.2
Title: S4 Class for Spatially Resolved -omics Data
Description: Defines an S4 class for storing data from spatial -omics experiments. 
 The class extends SingleCellExperiment to
 The class extends SingleCellExperiment to
 support storage and retrieval of additional information from spot-based and 
 molecule-based platforms, including spatial coordinates, images, and 
 image metadata. A specialized constructor function is included for data 
Expand Down

2 changes: 1 addition & 1 deletion
R/AllGenerics.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -51,7 +51,7 @@ setGeneric("spatialDataNames<-", function(x, value) standardGeneric("spatialData
setGeneric("spatialCoords", function(x, ...) standardGeneric("spatialCoords"))

#' @export
setGeneric("spatialCoords<-", function(x, value) standardGeneric("spatialCoords<-"))
setGeneric("spatialCoords<-", function(x, ..., value) standardGeneric("spatialCoords<-"))

#' @export
setGeneric("spatialCoordsNames", function(x) standardGeneric("spatialCoordsNames"))
Expand Down

5 changes: 5 additions & 0 deletions
R/SpatialExperiment-combine.R → R/SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -103,6 +103,11 @@ setMethod("cbind", "SpatialExperiment", function(..., deparse.level=1) {
 out <- do.call(
 callNextMethod, 
 c(args, list(deparse.level=1)))
 if (any(duplicated(colnames(out)))) {
 n <- vapply(args, ncol, integer(1))
 n <- rep.int(seq_along(args), n)
 colnames(out) <- paste(n, colnames(out), sep="_")
 }

 # merge 'imgData' from multiple samples
 if (!is.null(imgData(args[[1]]))) { 
Expand Down

70 changes: 7 additions & 63 deletions
R/SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -23,7 +23,14 @@
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all samples).
#' @param image_id Logical value or character vector specifying image
#' identifier(s) for \code{scaleFactors}. Default = \code{TRUE} (all images).
#' @param withDimnames Logical value indicating whether dimnames of the
#' \code{spatialExperiment} should be applied or checked against.
#' If \code{withDimnames=TRUE}, non-\code{NULL} \code{rownames(value)} 
#' are checked against \code{colnames(x)}, and an error occurs if these
#' don't match. Else, discrepancies in rownames are ignored.
#' (see also \code{\link[SingleCellExperiment]{reducedDims}})
#' @param name The name of the \code{colData} column to extract.
#' @param ... Further arguments passed to and from other methods.
#' 
#' @details
#' Additional details for each type of data attribute are provided below.
Expand DownExpand Up@@ -190,69 +197,6 @@ setReplaceMethod("spatialDataNames",
 }
)

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x) int_colData(x)$spatialCoords)

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
 function(x, value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, value) {
 value <- matrix(numeric(), ncol(x), 0)
 `spatialCoords<-`(x, value)
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

# scaleFactors -----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
Expand Down

8 changes: 3 additions & 5 deletions
R/read10xVisium.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,13 +195,11 @@ read10xVisium <- function(samples="",
 cnms <- c(
 "barcode", "in_tissue", "array_row", "array_col", 
 "pxl_row_in_fullres", "pxl_col_in_fullres")
 df <- lapply(seq_along(x), function(i) 
 {
 df <- read.csv(x[i], 
 header=!grepl("list", x[i]), 
 row.names=1, col.names=cnms)
 df <- lapply(seq_along(x), function(i) {
 df <- read.csv(x[i], header=!grepl("list", x[i]), col.names=cnms)
 if (length(x) > 1) rownames(df) <- paste(i, rownames(df), sep="_")
 if (!is.null(names(x))) cbind(sample_id=names(x)[i], df)
 rownames(df) <- df$barcode
 df
 })
 df <- do.call(rbind, df)
Expand Down

77 changes: 77 additions & 0 deletions
R/spatialCoords.R

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,77 @@

# spatialCoords ----------------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setMethod("spatialCoords", 
 "SpatialExperiment",
 function(x, withDimnames=TRUE, ...) {
 out <- int_colData(x)$spatialCoords
 if (withDimnames) 
 rownames(out) <- colnames(x)
 return(out)
 })

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "matrix"),
@drighellidrighelliNov 22, 2022

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there is a warning that I suppose is coming from the "matrix" instead of a "value"
Warning: ‘spatialCoords<-’
‘\S4method{spatialCoords<-}{SpatialExperiment,NULL}’
‘\S4method{spatialCoords<-}{SpatialExperiment,matrix}’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.

@HelenaLCHelenaLCNov 22, 2022

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Yeah I saw. But I don’t understand because it’s good locally. I’m on it…
@drighellidrighelliNov 22, 2022

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indeed I don't get why, but have you tried something like: c("SpatialExperiment", "value") ?
@drighellidrighelliNov 22, 2022

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I think that's because the generic is defined as setGeneric("spatialCoords<-", function(x, value, withDimnames=TRUE) standardGeneric("spatialCoords<-"))
@HelenaLCHelenaLCNov 22, 2022•

edited

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…the signature has to be classes, so “NULL” and “matrix” (not “value”) is correct. It’s saying the generic and methods don’t match. But I don’t see why not as they both have “value” in the function definition in the same order…
@drighellidrighelliNov 23, 2022

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yes, I saw that, I'm looking over the internet, but still I'm not able to understand the motivation for this warning.
 function(x, withDimnames=TRUE, ..., value) {
 stopifnot(
 is.numeric(value),
 nrow(value) == ncol(x))
 new <- rownames(value)
 if (!is.null(new) && withDimnames) {
 if (!identical(new, colnames(x))) {
 stop("Non-NULL 'rownames(value)' should be the",
 " same as 'colnames(x)' for 'spatialCoords<-'.",
 " Use 'withDimnames=FALSE' to force replacement.")
 }
 }
 int_colData(x)$spatialCoords <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoords", 
 c("SpatialExperiment", "NULL"),
 function(x, withDimnames=TRUE, ..., value) {
 `spatialCoords<-`(x, 
 withDimnames=withDimnames, ..., 
 value=matrix(numeric(), ncol(x), 0))
 }
)

# spatialCoordsNames -----------------------------------------------------------

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData
#' @export
setMethod("spatialCoordsNames", 
 "SpatialExperiment", 
 function(x) colnames(int_colData(x)$spatialCoords))

#' @rdname SpatialExperiment-methods
#' @importFrom SingleCellExperiment int_colData<-
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "character"), 
 function(x, value) {
 colnames(int_colData(x)$spatialCoords) <- value
 return(x)
 }
)

#' @rdname SpatialExperiment-methods
#' @export
setReplaceMethod("spatialCoordsNames", 
 c("SpatialExperiment", "NULL"), 
 function(x, value) {
 value <- character()
 `spatialCoordsNames<-`(x, value)
 }
)

6 changes: 6 additions & 0 deletions
inst/NEWS

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,6 +8,12 @@ changes in version 1.9.5 (2023-03-02)
+ bugfix for tissue positions read in incorrect order with read10xVisium() in 
 datasets with multiple samples (bug introduced in version 1.7.1)

changes in version 1.9.4 (2022-11-24)
+ avoid duplicated colnames when cbinding SPEs
+ read10xVisium keeps original barcodes as colData
+ added withDimnames argument for spatialCoords/<-
 (analogous to SCE's reducedDim(s)/<-)

changes in version 1.7.2 (2022-10-07)
+ support for seeing colData names with $ in RStudio

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2 changes: 1 addition & 1 deletion
man/SpatialExperiment-combine.Rd

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44 changes: 27 additions & 17 deletions
man/SpatialExperiment-methods.Rd

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13 changes: 12 additions & 1 deletion
tests/testthat/test_SpatialExperiment-cbind.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -8,7 +8,6 @@ test_that("duplicated sample_ids are made unique with a message", {
 expect_true(nrow(new) == nrow(spe))
 expect_true(ncol(new) == 2*ncol(spe))
 expect_identical(rownames(new), rownames(spe))
 expect_setequal(colnames(new), colnames(spe))
})

test_that("imgData are combined correctly", {
Expand All@@ -33,3 +32,15 @@ test_that("imgData are combined correctly", {
 expect_identical(imgData(spe3)[one, ], imgData(spe1))
 expect_identical(imgData(spe3)[two, ], imgData(spe2))
})

test_that("unique colnames are left asis,", {
 tmp <- spe
 colnames(tmp) <- paste0(colnames(tmp), "x")
 out <- cbind(spe, tmp)
 expect_false(any(duplicated(colnames(out))))
})

test_that("duplicated colnames are made unique", {
 out <- cbind(spe, spe)
 expect_false(any(duplicated(colnames(out))))
})

22 changes: 0 additions & 22 deletions
tests/testthat/test_SpatialExperiment-methods.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -45,28 +45,6 @@ test_that("spatialDataNames()<-,NULL", {
 expect_identical(new, character(0))
})

test_that("spatialCoordsNames()", {
 expect_identical(
 spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,character", {
 old <- spatialCoordsNames(spe)
 new <- sample(letters, length(old))
 spatialCoordsNames(spe) <- new
 expect_identical(spatialCoordsNames(spe), new)
 expect_identical(spatialCoordsNames(spe), 
 colnames(int_colData(spe)$spatialCoords))
})

test_that("spatialCoordsNames<-,NULL", {
 old <- spatialCoords(spe)
 spatialCoordsNames(spe) <- NULL
 expect_null(spatialCoordsNames(spe))
 expect_equivalent(spatialCoords(spe), old)
})

test_that("scaleFactors()", {
 sfs <- scaleFactors(spe, sample_id=TRUE, image_id=TRUE)
 expect_is(sfs, "numeric")
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