claude code's initial build#1

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Merged
msraredon merged 2 commits into from
Apr 4, 2026
Merged

claude code's initial build #1

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6044f41
initial files, migrated from tissue field
msraredon Apr 4, 2026
1e0479e
claude code's initial build
msraredon Apr 4, 2026
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13 changes: 13 additions & 0 deletions .Rbuildignore
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$
52 changes: 52 additions & 0 deletions .github/workflows/R-CMD-check.yaml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
push:
branches: [main, master]
pull_request:
branches: [main, master]

name: R-CMD-check

jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}

name: ${{ matrix.config.os }} (${{ matrix.config.r }})

strategy:
fail-fast: false
matrix:
config:
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check

- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
args: 'c("--no-manual", "--as-cran")'
52 changes: 52 additions & 0 deletions .github/workflows/pkgdown.yaml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
push:
branches: [main, master]
release:
types: [published]
workflow_dispatch:

name: pkgdown

concurrency:
group: pkgdown-${{ github.event_name }}
cancel-in-progress: true

jobs:
pkgdown:
runs-on: ubuntu-latest

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

permissions:
contents: write

steps:
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::pkgdown, local::.
needs: website

- name: Build site
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}

- name: Deploy to GitHub pages
uses: JamesIves/github-pages-deploy-action@v4
with:
clean: false
branch: gh-pages
folder: docs
37 changes: 37 additions & 0 deletions DESCRIPTION
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
cell centroids or transcript locations from spatial transcriptomics
and spatial proteomics experiments. Supports four methods of
increasing topological complexity: convex hull, concave hull, kernel
density estimation (KDE), and a raster-based Gaussian smoothing
approach that naturally handles internal voids (vessel lumens,
necrotic cores, tissue tears) and disconnected tissue islands via
GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
R (>= 4.1.0)
Imports:
sf (>= 1.0-0),
stats,
parallel
Suggests:
concaveman,
MASS,
isoband,
ggplot2,
testthat (>= 3.0.0),
knitr,
rmarkdown,
patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3
24 changes: 24 additions & 0 deletions NAMESPACE
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)
28 changes: 28 additions & 0 deletions R/TissueMask-package.R
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Open in desktop
Original file line numberDiff line numberDiff line change
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#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
claude code's initial build#1

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privacy statement. We’ll occasionally send you account related emails.

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Sign in
to your account

 Merged

msraredon
merged 2 commits into

from

Apr 4, 2026
 Merged


claude code's initial build
#1
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6044f41

initial files, migrated from tissue field


msraredon Apr 4, 2026
1e0479e

claude code's initial build


msraredon Apr 4, 2026

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13 changes: 13 additions & 0 deletions
.Rbuildignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$

52 changes: 52 additions & 0 deletions
.github/workflows/R-CMD-check.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
 push:
 branches: [main, master]
 pull_request:
 branches: [main, master]

name: R-CMD-check

jobs:
 R-CMD-check:
 runs-on: ${{ matrix.config.os }}

 name: ${{ matrix.config.os }} (${{ matrix.config.r }})

 strategy:
 fail-fast: false
 matrix:
 config:
 - {os: ubuntu-latest, r: 'release'}
 - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 - {os: macos-latest, r: 'release'}
 - {os: windows-latest, r: 'release'}

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 R_KEEP_PKG_SOURCE: yes

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 r-version: ${{ matrix.config.r }}
 http-user-agent: ${{ matrix.config.http-user-agent }}
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::rcmdcheck
 needs: check

 - uses: r-lib/actions/check-r-package@v2
 with:
 upload-snapshots: true
 build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
 args: 'c("--no-manual", "--as-cran")'

52 changes: 52 additions & 0 deletions
.github/workflows/pkgdown.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
 push:
 branches: [main, master]
 release:
 types: [published]
 workflow_dispatch:

name: pkgdown

concurrency:
 group: pkgdown-${{ github.event_name }}
 cancel-in-progress: true

jobs:
 pkgdown:
 runs-on: ubuntu-latest

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

 permissions:
 contents: write

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::pkgdown, local::.
 needs: website

 - name: Build site
 run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 shell: Rscript {0}

 - name: Deploy to GitHub pages
 uses: JamesIves/github-pages-deploy-action@v4
 with:
 clean: false
 branch: gh-pages
 folder: docs

37 changes: 37 additions & 0 deletions
DESCRIPTION

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
 email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
 cell centroids or transcript locations from spatial transcriptomics
 and spatial proteomics experiments. Supports four methods of
 increasing topological complexity: convex hull, concave hull, kernel
 density estimation (KDE), and a raster-based Gaussian smoothing
 approach that naturally handles internal voids (vessel lumens,
 necrotic cores, tissue tears) and disconnected tissue islands via
 GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
 R (>= 4.1.0)
Imports:
 sf (>= 1.0-0),
 stats,
 parallel
Suggests:
 concaveman,
 MASS,
 isoband,
 ggplot2,
 testthat (>= 3.0.0),
 knitr,
 rmarkdown,
 patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3

24 changes: 24 additions & 0 deletions
NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)

28 changes: 28 additions & 0 deletions
R/TissueMask-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
claude code's initial build#1

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Already on GitHub?
Sign in
to your account

 Merged

msraredon
merged 2 commits into

from

Apr 4, 2026
 Merged


claude code's initial build
#1
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6044f41

initial files, migrated from tissue field


msraredon Apr 4, 2026
1e0479e

claude code's initial build


msraredon Apr 4, 2026

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13 changes: 13 additions & 0 deletions
.Rbuildignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$

52 changes: 52 additions & 0 deletions
.github/workflows/R-CMD-check.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
 push:
 branches: [main, master]
 pull_request:
 branches: [main, master]

name: R-CMD-check

jobs:
 R-CMD-check:
 runs-on: ${{ matrix.config.os }}

 name: ${{ matrix.config.os }} (${{ matrix.config.r }})

 strategy:
 fail-fast: false
 matrix:
 config:
 - {os: ubuntu-latest, r: 'release'}
 - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 - {os: macos-latest, r: 'release'}
 - {os: windows-latest, r: 'release'}

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 R_KEEP_PKG_SOURCE: yes

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 r-version: ${{ matrix.config.r }}
 http-user-agent: ${{ matrix.config.http-user-agent }}
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::rcmdcheck
 needs: check

 - uses: r-lib/actions/check-r-package@v2
 with:
 upload-snapshots: true
 build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
 args: 'c("--no-manual", "--as-cran")'

52 changes: 52 additions & 0 deletions
.github/workflows/pkgdown.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
 push:
 branches: [main, master]
 release:
 types: [published]
 workflow_dispatch:

name: pkgdown

concurrency:
 group: pkgdown-${{ github.event_name }}
 cancel-in-progress: true

jobs:
 pkgdown:
 runs-on: ubuntu-latest

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

 permissions:
 contents: write

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::pkgdown, local::.
 needs: website

 - name: Build site
 run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 shell: Rscript {0}

 - name: Deploy to GitHub pages
 uses: JamesIves/github-pages-deploy-action@v4
 with:
 clean: false
 branch: gh-pages
 folder: docs

37 changes: 37 additions & 0 deletions
DESCRIPTION

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
 email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
 cell centroids or transcript locations from spatial transcriptomics
 and spatial proteomics experiments. Supports four methods of
 increasing topological complexity: convex hull, concave hull, kernel
 density estimation (KDE), and a raster-based Gaussian smoothing
 approach that naturally handles internal voids (vessel lumens,
 necrotic cores, tissue tears) and disconnected tissue islands via
 GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
 R (>= 4.1.0)
Imports:
 sf (>= 1.0-0),
 stats,
 parallel
Suggests:
 concaveman,
 MASS,
 isoband,
 ggplot2,
 testthat (>= 3.0.0),
 knitr,
 rmarkdown,
 patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3

24 changes: 24 additions & 0 deletions
NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)

28 changes: 28 additions & 0 deletions
R/TissueMask-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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msraredon
merged 2 commits into

from

Apr 4, 2026
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claude code's initial build
#1
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6044f41

initial files, migrated from tissue field


msraredon Apr 4, 2026
1e0479e

claude code's initial build


msraredon Apr 4, 2026

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13 changes: 13 additions & 0 deletions
.Rbuildignore

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$

52 changes: 52 additions & 0 deletions
.github/workflows/R-CMD-check.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
 push:
 branches: [main, master]
 pull_request:
 branches: [main, master]

name: R-CMD-check

jobs:
 R-CMD-check:
 runs-on: ${{ matrix.config.os }}

 name: ${{ matrix.config.os }} (${{ matrix.config.r }})

 strategy:
 fail-fast: false
 matrix:
 config:
 - {os: ubuntu-latest, r: 'release'}
 - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 - {os: macos-latest, r: 'release'}
 - {os: windows-latest, r: 'release'}

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 R_KEEP_PKG_SOURCE: yes

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 r-version: ${{ matrix.config.r }}
 http-user-agent: ${{ matrix.config.http-user-agent }}
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::rcmdcheck
 needs: check

 - uses: r-lib/actions/check-r-package@v2
 with:
 upload-snapshots: true
 build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
 args: 'c("--no-manual", "--as-cran")'

52 changes: 52 additions & 0 deletions
.github/workflows/pkgdown.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
 push:
 branches: [main, master]
 release:
 types: [published]
 workflow_dispatch:

name: pkgdown

concurrency:
 group: pkgdown-${{ github.event_name }}
 cancel-in-progress: true

jobs:
 pkgdown:
 runs-on: ubuntu-latest

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

 permissions:
 contents: write

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::pkgdown, local::.
 needs: website

 - name: Build site
 run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 shell: Rscript {0}

 - name: Deploy to GitHub pages
 uses: JamesIves/github-pages-deploy-action@v4
 with:
 clean: false
 branch: gh-pages
 folder: docs

37 changes: 37 additions & 0 deletions
DESCRIPTION

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
 email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
 cell centroids or transcript locations from spatial transcriptomics
 and spatial proteomics experiments. Supports four methods of
 increasing topological complexity: convex hull, concave hull, kernel
 density estimation (KDE), and a raster-based Gaussian smoothing
 approach that naturally handles internal voids (vessel lumens,
 necrotic cores, tissue tears) and disconnected tissue islands via
 GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
 R (>= 4.1.0)
Imports:
 sf (>= 1.0-0),
 stats,
 parallel
Suggests:
 concaveman,
 MASS,
 isoband,
 ggplot2,
 testthat (>= 3.0.0),
 knitr,
 rmarkdown,
 patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3

24 changes: 24 additions & 0 deletions
NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)

28 changes: 28 additions & 0 deletions
R/TissueMask-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
claude code's initial build#1

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

msraredon
merged 2 commits into

from

Apr 4, 2026
 Merged


claude code's initial build
#1
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6044f41

initial files, migrated from tissue field


msraredon Apr 4, 2026
1e0479e

claude code's initial build


msraredon Apr 4, 2026

File filter

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13 changes: 13 additions & 0 deletions
.Rbuildignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$

52 changes: 52 additions & 0 deletions
.github/workflows/R-CMD-check.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
 push:
 branches: [main, master]
 pull_request:
 branches: [main, master]

name: R-CMD-check

jobs:
 R-CMD-check:
 runs-on: ${{ matrix.config.os }}

 name: ${{ matrix.config.os }} (${{ matrix.config.r }})

 strategy:
 fail-fast: false
 matrix:
 config:
 - {os: ubuntu-latest, r: 'release'}
 - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 - {os: macos-latest, r: 'release'}
 - {os: windows-latest, r: 'release'}

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 R_KEEP_PKG_SOURCE: yes

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 r-version: ${{ matrix.config.r }}
 http-user-agent: ${{ matrix.config.http-user-agent }}
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::rcmdcheck
 needs: check

 - uses: r-lib/actions/check-r-package@v2
 with:
 upload-snapshots: true
 build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
 args: 'c("--no-manual", "--as-cran")'

52 changes: 52 additions & 0 deletions
.github/workflows/pkgdown.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
 push:
 branches: [main, master]
 release:
 types: [published]
 workflow_dispatch:

name: pkgdown

concurrency:
 group: pkgdown-${{ github.event_name }}
 cancel-in-progress: true

jobs:
 pkgdown:
 runs-on: ubuntu-latest

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

 permissions:
 contents: write

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::pkgdown, local::.
 needs: website

 - name: Build site
 run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 shell: Rscript {0}

 - name: Deploy to GitHub pages
 uses: JamesIves/github-pages-deploy-action@v4
 with:
 clean: false
 branch: gh-pages
 folder: docs

37 changes: 37 additions & 0 deletions
DESCRIPTION

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
 email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
 cell centroids or transcript locations from spatial transcriptomics
 and spatial proteomics experiments. Supports four methods of
 increasing topological complexity: convex hull, concave hull, kernel
 density estimation (KDE), and a raster-based Gaussian smoothing
 approach that naturally handles internal voids (vessel lumens,
 necrotic cores, tissue tears) and disconnected tissue islands via
 GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
 R (>= 4.1.0)
Imports:
 sf (>= 1.0-0),
 stats,
 parallel
Suggests:
 concaveman,
 MASS,
 isoband,
 ggplot2,
 testthat (>= 3.0.0),
 knitr,
 rmarkdown,
 patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3

24 changes: 24 additions & 0 deletions
NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)

28 changes: 28 additions & 0 deletions
R/TissueMask-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
claude code's initial build#1

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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Already on GitHub?
Sign in
to your account

 Merged

msraredon
merged 2 commits into

from

Apr 4, 2026
 Merged


claude code's initial build
#1
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6044f41

initial files, migrated from tissue field


msraredon Apr 4, 2026
1e0479e

claude code's initial build


msraredon Apr 4, 2026

File filter

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13 changes: 13 additions & 0 deletions
.Rbuildignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$

52 changes: 52 additions & 0 deletions
.github/workflows/R-CMD-check.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
 push:
 branches: [main, master]
 pull_request:
 branches: [main, master]

name: R-CMD-check

jobs:
 R-CMD-check:
 runs-on: ${{ matrix.config.os }}

 name: ${{ matrix.config.os }} (${{ matrix.config.r }})

 strategy:
 fail-fast: false
 matrix:
 config:
 - {os: ubuntu-latest, r: 'release'}
 - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 - {os: macos-latest, r: 'release'}
 - {os: windows-latest, r: 'release'}

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 R_KEEP_PKG_SOURCE: yes

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 r-version: ${{ matrix.config.r }}
 http-user-agent: ${{ matrix.config.http-user-agent }}
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::rcmdcheck
 needs: check

 - uses: r-lib/actions/check-r-package@v2
 with:
 upload-snapshots: true
 build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
 args: 'c("--no-manual", "--as-cran")'

52 changes: 52 additions & 0 deletions
.github/workflows/pkgdown.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
 push:
 branches: [main, master]
 release:
 types: [published]
 workflow_dispatch:

name: pkgdown

concurrency:
 group: pkgdown-${{ github.event_name }}
 cancel-in-progress: true

jobs:
 pkgdown:
 runs-on: ubuntu-latest

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

 permissions:
 contents: write

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::pkgdown, local::.
 needs: website

 - name: Build site
 run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 shell: Rscript {0}

 - name: Deploy to GitHub pages
 uses: JamesIves/github-pages-deploy-action@v4
 with:
 clean: false
 branch: gh-pages
 folder: docs

37 changes: 37 additions & 0 deletions
DESCRIPTION

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
 email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
 cell centroids or transcript locations from spatial transcriptomics
 and spatial proteomics experiments. Supports four methods of
 increasing topological complexity: convex hull, concave hull, kernel
 density estimation (KDE), and a raster-based Gaussian smoothing
 approach that naturally handles internal voids (vessel lumens,
 necrotic cores, tissue tears) and disconnected tissue islands via
 GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
 R (>= 4.1.0)
Imports:
 sf (>= 1.0-0),
 stats,
 parallel
Suggests:
 concaveman,
 MASS,
 isoband,
 ggplot2,
 testthat (>= 3.0.0),
 knitr,
 rmarkdown,
 patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3

24 changes: 24 additions & 0 deletions
NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)

28 changes: 28 additions & 0 deletions
R/TissueMask-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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to your account

 Merged

msraredon
merged 2 commits into

from

Apr 4, 2026
 Merged


claude code's initial build
#1
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6044f41

initial files, migrated from tissue field


msraredon Apr 4, 2026
1e0479e

claude code's initial build


msraredon Apr 4, 2026

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13 changes: 13 additions & 0 deletions
.Rbuildignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$

52 changes: 52 additions & 0 deletions
.github/workflows/R-CMD-check.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
 push:
 branches: [main, master]
 pull_request:
 branches: [main, master]

name: R-CMD-check

jobs:
 R-CMD-check:
 runs-on: ${{ matrix.config.os }}

 name: ${{ matrix.config.os }} (${{ matrix.config.r }})

 strategy:
 fail-fast: false
 matrix:
 config:
 - {os: ubuntu-latest, r: 'release'}
 - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 - {os: macos-latest, r: 'release'}
 - {os: windows-latest, r: 'release'}

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 R_KEEP_PKG_SOURCE: yes

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 r-version: ${{ matrix.config.r }}
 http-user-agent: ${{ matrix.config.http-user-agent }}
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::rcmdcheck
 needs: check

 - uses: r-lib/actions/check-r-package@v2
 with:
 upload-snapshots: true
 build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
 args: 'c("--no-manual", "--as-cran")'

52 changes: 52 additions & 0 deletions
.github/workflows/pkgdown.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
 push:
 branches: [main, master]
 release:
 types: [published]
 workflow_dispatch:

name: pkgdown

concurrency:
 group: pkgdown-${{ github.event_name }}
 cancel-in-progress: true

jobs:
 pkgdown:
 runs-on: ubuntu-latest

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

 permissions:
 contents: write

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::pkgdown, local::.
 needs: website

 - name: Build site
 run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 shell: Rscript {0}

 - name: Deploy to GitHub pages
 uses: JamesIves/github-pages-deploy-action@v4
 with:
 clean: false
 branch: gh-pages
 folder: docs

37 changes: 37 additions & 0 deletions
DESCRIPTION

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
 email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
 cell centroids or transcript locations from spatial transcriptomics
 and spatial proteomics experiments. Supports four methods of
 increasing topological complexity: convex hull, concave hull, kernel
 density estimation (KDE), and a raster-based Gaussian smoothing
 approach that naturally handles internal voids (vessel lumens,
 necrotic cores, tissue tears) and disconnected tissue islands via
 GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
 R (>= 4.1.0)
Imports:
 sf (>= 1.0-0),
 stats,
 parallel
Suggests:
 concaveman,
 MASS,
 isoband,
 ggplot2,
 testthat (>= 3.0.0),
 knitr,
 rmarkdown,
 patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3

24 changes: 24 additions & 0 deletions
NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)

28 changes: 28 additions & 0 deletions
R/TissueMask-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
claude code's initial build#1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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Sign in
to your account

 Merged

msraredon
merged 2 commits into

from

Apr 4, 2026
 Merged


claude code's initial build
#1
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6044f41

initial files, migrated from tissue field


msraredon Apr 4, 2026
1e0479e

claude code's initial build


msraredon Apr 4, 2026

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13 changes: 13 additions & 0 deletions
.Rbuildignore

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
^fit_spatial_mask\.R$
^demo_fit_spatial_mask\.R$
^demo_holes_and_scale\.R$
^vignette_fit_spatial_mask\.Rmd$
^vignette_fit_spatial_mask\.html$
^vignette_fit_spatial_mask_cache$
^vignette_fit_spatial_mask_files$
^_pkgdown\.yml$
^pkgdown$
^\.github$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$

52 changes: 52 additions & 0 deletions
.github/workflows/R-CMD-check.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# R CMD check workflow
# Runs on every push and pull request to main/master.
# Tests on Ubuntu (release + devel), macOS (release), and Windows (release).

on:
 push:
 branches: [main, master]
 pull_request:
 branches: [main, master]

name: R-CMD-check

jobs:
 R-CMD-check:
 runs-on: ${{ matrix.config.os }}

 name: ${{ matrix.config.os }} (${{ matrix.config.r }})

 strategy:
 fail-fast: false
 matrix:
 config:
 - {os: ubuntu-latest, r: 'release'}
 - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
 - {os: macos-latest, r: 'release'}
 - {os: windows-latest, r: 'release'}

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 R_KEEP_PKG_SOURCE: yes

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 r-version: ${{ matrix.config.r }}
 http-user-agent: ${{ matrix.config.http-user-agent }}
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::rcmdcheck
 needs: check

 - uses: r-lib/actions/check-r-package@v2
 with:
 upload-snapshots: true
 build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
 args: 'c("--no-manual", "--as-cran")'

52 changes: 52 additions & 0 deletions
.github/workflows/pkgdown.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
# pkgdown site deployment
# Builds and deploys the pkgdown site to GitHub Pages on every push to main.
# Requires GitHub Pages to be enabled with "Source: Deploy from a branch"
# set to "gh-pages / (root)" in repository Settings > Pages.

on:
 push:
 branches: [main, master]
 release:
 types: [published]
 workflow_dispatch:

name: pkgdown

concurrency:
 group: pkgdown-${{ github.event_name }}
 cancel-in-progress: true

jobs:
 pkgdown:
 runs-on: ubuntu-latest

 env:
 GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

 permissions:
 contents: write

 steps:
 - uses: actions/checkout@v4

 - uses: r-lib/actions/setup-pandoc@v2

 - uses: r-lib/actions/setup-r@v2
 with:
 use-public-rspm: true

 - uses: r-lib/actions/setup-r-dependencies@v2
 with:
 extra-packages: any::pkgdown, local::.
 needs: website

 - name: Build site
 run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
 shell: Rscript {0}

 - name: Deploy to GitHub pages
 uses: JamesIves/github-pages-deploy-action@v4
 with:
 clean: false
 branch: gh-pages
 folder: docs

37 changes: 37 additions & 0 deletions
DESCRIPTION

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,37 @@
Package: TissueMask
Type: Package
Title: Spatial Boundary Mask Fitting for Point Coordinate Data
Version: 0.1.0
Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
 email = "raredonlab@yale.edu")
Description: Fits polygon spatial masks to XY point coordinates such as
 cell centroids or transcript locations from spatial transcriptomics
 and spatial proteomics experiments. Supports four methods of
 increasing topological complexity: convex hull, concave hull, kernel
 density estimation (KDE), and a raster-based Gaussian smoothing
 approach that naturally handles internal voids (vessel lumens,
 necrotic cores, tissue tears) and disconnected tissue islands via
 GEOS polygon dissolve.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
 R (>= 4.1.0)
Imports:
 sf (>= 1.0-0),
 stats,
 parallel
Suggests:
 concaveman,
 MASS,
 isoband,
 ggplot2,
 testthat (>= 3.0.0),
 knitr,
 rmarkdown,
 patchwork
VignetteBuilder: knitr
URL: https://raredonlab.github.io/TissueMask/, https://github.com/RaredonLab/TissueMask
BugReports: https://github.com/RaredonLab/TissueMask/issues
Config/testthat/edition: 3

24 changes: 24 additions & 0 deletions
NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
# Generated by roxygen2: do not edit by hand

export(fit_spatial_mask)
importFrom(parallel,mclapply)
importFrom(sf,NA_crs_)
importFrom(sf,st_area)
importFrom(sf,st_as_sf)
importFrom(sf,st_bbox)
importFrom(sf,st_buffer)
importFrom(sf,st_convex_hull)
importFrom(sf,"st_crs<-")
importFrom(sf,st_difference)
importFrom(sf,st_distance)
importFrom(sf,st_geometry)
importFrom(sf,st_make_valid)
importFrom(sf,st_polygon)
importFrom(sf,st_sf)
importFrom(sf,st_sfc)
importFrom(sf,st_simplify)
importFrom(sf,st_union)
importFrom(sf,st_within)
importFrom(stats,complete.cases)
importFrom(stats,filter)
importFrom(stats,quantile)

28 changes: 28 additions & 0 deletions
R/TissueMask-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
#' TissueMask: Spatial Boundary Mask Fitting for Point Coordinate Data
#'
#' @description
#' TissueMask provides [`fit_spatial_mask()`], which fits polygon spatial masks
#' to XY point coordinate data such as cell centroids or transcript locations
#' from spatial transcriptomics and spatial proteomics experiments.
#'
#' Four masking methods are available, supporting geometries of increasing
#' topological complexity — from simple convex hulls to multi-polygon masks
#' with internal voids and disconnected islands:
#'
#' | Method | Holes/Islands | Speed | Recommended for |
#' |---|---|---|---|
#' | `"convex"` | No | Instant | Sanity checks |
#' | `"concave"` | No | Fast | Simple non-convex shapes |
#' | `"kde"` | Yes | Moderate | Dense, smooth datasets |
#' | `"raster"` | Yes | Fast | Most use cases (default) |
#'
#' @section Part of TissueSuite:
#' TissueMask is the first component of the **TissueSuite** package family
#' developed at the Raredon Laboratory, Yale School of Medicine. The companion
#' package **TissueField** uses TissueMask output to estimate steady-state
#' molecular concentration fields via a diffusion–clearance PDE.
#'
#' @seealso [`fit_spatial_mask()`]
#'
#' @keywords internal
"_PACKAGE"
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