Fix var plotting#236

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Merged
melonora merged 8 commits into from
Apr 4, 2024
Merged

Fix var plotting #236

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f0452d4
fix var colorbar labels
melonora Mar 31, 2024
6f63830
fix var plotting in case of vector length 3/4
melonora Apr 1, 2024
9445e36
fix tests
melonora Apr 1, 2024
3d68be0
address comments
melonora Apr 4, 2024
5793bf2
remove unnecessary check
melonora Apr 4, 2024
c33f84a
more informative name
melonora Apr 4, 2024
56ed753
fix prettier
melonora Apr 4, 2024
46448b9
Merge branch 'main' into fix_var_plotting
melonora Apr 4, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

Expand Down
21 changes: 10 additions & 11 deletions src/spatialdata_plot/pl/render.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
na_color=render_params.cmap_params.na_color,
)

_cax = ax.imshow(
labels_infill,
rasterized=True,
cmap=None if categorical else render_params.cmap_params.cmap,
norm=None if categorical else render_params.cmap_params.norm,
alpha=render_params.fill_alpha,
origin="lower",
)
_cax.set_transform(trans_data)
cax = ax.add_image(_cax)

# Then overlay the contour
labels_contour = _map_color_seg(
seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
alpha=render_params.outline_alpha,
origin="lower",
)
_cax = ax.imshow(
labels_infill,
rasterized=True,
cmap=None if categorical else render_params.cmap_params.cmap,
norm=None if categorical else render_params.cmap_params.norm,
alpha=render_params.fill_alpha,
origin="lower",
)
_cax.set_transform(trans_data)
cax = ax.add_image(_cax)
else:
# Default: no alpha, contour = infill
label = _map_color_seg(
Expand Down
25 changes: 19 additions & 6 deletions src/spatialdata_plot/pl/utils.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

try:
# fails when numeric
fill_c = ColorConverter().to_rgba_array(c)
if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
if norm is None:
c = cmap(c)
else:
try:
norm = colors.Normalize(vmin=min(c), vmax=max(c))
except ValueError as e:
raise ValueError(
"Could not convert values in the `color` column to float, if `color` column represents"
" categories, set the column to categorical dtype."
) from e
c = cmap(norm(c))
else:
fill_c = ColorConverter().to_rgba_array(c)
except ValueError:
if norm is None:
c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
ax: Axes,
cax: PatchCollection,
fig_params: FigParams,
value_to_plot: str | None, # str | None,
value_to_plot: str | None,
color_source_vector: pd.Series[CategoricalDtype],
adata: AnnData | None = None,
palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
params.col_for_color.append(col_color)
element_table_mapping[element_name] = set()
else:
if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
for table_name in mapping.copy():
if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
for table_name in table_set.copy():
if (
col_color not in sdata[table_name].obs.columns
and col_color not in sdata[table_name].var_names
):
mapping.remove(table_name)
table_set.remove(table_name)
params.col_for_color.append(None)
else:
params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
"""Force mypy to recognize list of string and None."""
if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
checked_parameter = parameter if isinstance(parameter, list) else [None]
checked_parameter = parameter
else:
checked_parameter = [None]
return checked_parameter
Expand Down
, '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
Fix var plotting#236

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 Merged

melonora
merged 8 commits into

from

Apr 4, 2024
 Merged


Fix var plotting
#236
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f0452d4

fix var colorbar labels


melonora Mar 31, 2024
6f63830

fix var plotting in case of vector length 3/4


melonora Apr 1, 2024
9445e36

fix tests


melonora Apr 1, 2024
3d68be0

address comments


melonora Apr 4, 2024
5793bf2

remove unnecessary check


melonora Apr 4, 2024
c33f84a

more informative name


melonora Apr 4, 2024
56ed753

fix prettier


melonora Apr 4, 2024
46448b9

Merge branch 'main' into fix_var_plotting


melonora Apr 4, 2024

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2 changes: 1 addition & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

Expand Down

21 changes: 10 additions & 11 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
 na_color=render_params.cmap_params.na_color,
 )

 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)

 # Then overlay the contour
 labels_contour = _map_color_seg(
 seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
 alpha=render_params.outline_alpha,
 origin="lower",
 )
 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 else:
 # Default: no alpha, contour = infill
 label = _map_color_seg(
Expand Down

25 changes: 19 additions & 6 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

 try:
 # fails when numeric
 fill_c = ColorConverter().to_rgba_array(c)
 if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
 if norm is None:
 c = cmap(c)
 else:
 try:
 norm = colors.Normalize(vmin=min(c), vmax=max(c))
 except ValueError as e:
 raise ValueError(
 "Could not convert values in the `color` column to float, if `color` column represents"
 " categories, set the column to categorical dtype."
 ) from e
 c = cmap(norm(c))
 else:
 fill_c = ColorConverter().to_rgba_array(c)
 except ValueError:
 if norm is None:
 c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
 ax: Axes,
 cax: PatchCollection,
 fig_params: FigParams,
 value_to_plot: str | None, # str | None,
 value_to_plot: str | None,
 color_source_vector: pd.Series[CategoricalDtype],
 adata: AnnData | None = None,
 palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
 params.col_for_color.append(col_color)
 element_table_mapping[element_name] = set()
 else:
 if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
 for table_name in mapping.copy():
 if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
 for table_name in table_set.copy():
 if (
 col_color not in sdata[table_name].obs.columns
 and col_color not in sdata[table_name].var_names
 ):
mapping.remove(table_name)
table_set.remove(table_name)
 params.col_for_color.append(None)
 else:
 params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
 """Force mypy to recognize list of string and None."""
 if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
 checked_parameter = parameter if isinstance(parameter, list) else [None]
 checked_parameter = parameter
 else:
 checked_parameter = [None]
 return checked_parameter
Expand Down

, '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
Fix var plotting#236

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.

 Sign up for GitHub

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

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Apr 4, 2024
 Merged


Fix var plotting
#236
Show file tree
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Commits

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8 commits


Select commit
Hold shift + click to select a range
f0452d4

fix var colorbar labels


melonora Mar 31, 2024
6f63830

fix var plotting in case of vector length 3/4


melonora Apr 1, 2024
9445e36

fix tests


melonora Apr 1, 2024
3d68be0

address comments


melonora Apr 4, 2024
5793bf2

remove unnecessary check


melonora Apr 4, 2024
c33f84a

more informative name


melonora Apr 4, 2024
56ed753

fix prettier


melonora Apr 4, 2024
46448b9

Merge branch 'main' into fix_var_plotting


melonora Apr 4, 2024

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2 changes: 1 addition & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

Expand Down

21 changes: 10 additions & 11 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
 na_color=render_params.cmap_params.na_color,
 )

 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)

 # Then overlay the contour
 labels_contour = _map_color_seg(
 seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
 alpha=render_params.outline_alpha,
 origin="lower",
 )
 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 else:
 # Default: no alpha, contour = infill
 label = _map_color_seg(
Expand Down

25 changes: 19 additions & 6 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

 try:
 # fails when numeric
 fill_c = ColorConverter().to_rgba_array(c)
 if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
 if norm is None:
 c = cmap(c)
 else:
 try:
 norm = colors.Normalize(vmin=min(c), vmax=max(c))
 except ValueError as e:
 raise ValueError(
 "Could not convert values in the `color` column to float, if `color` column represents"
 " categories, set the column to categorical dtype."
 ) from e
 c = cmap(norm(c))
 else:
 fill_c = ColorConverter().to_rgba_array(c)
 except ValueError:
 if norm is None:
 c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
 ax: Axes,
 cax: PatchCollection,
 fig_params: FigParams,
 value_to_plot: str | None, # str | None,
 value_to_plot: str | None,
 color_source_vector: pd.Series[CategoricalDtype],
 adata: AnnData | None = None,
 palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
 params.col_for_color.append(col_color)
 element_table_mapping[element_name] = set()
 else:
 if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
 for table_name in mapping.copy():
 if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
 for table_name in table_set.copy():
 if (
 col_color not in sdata[table_name].obs.columns
 and col_color not in sdata[table_name].var_names
 ):
mapping.remove(table_name)
table_set.remove(table_name)
 params.col_for_color.append(None)
 else:
 params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
 """Force mypy to recognize list of string and None."""
 if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
 checked_parameter = parameter if isinstance(parameter, list) else [None]
 checked_parameter = parameter
 else:
 checked_parameter = [None]
 return checked_parameter
Expand Down

, '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('^' + ".*" + '

Skip to content
Fix var plotting#236

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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to your account

 Merged

melonora
merged 8 commits into

from

Apr 4, 2024
 Merged


Fix var plotting
#236
Show file tree
Hide file tree
 Changes from all commits
Commits

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8 commits


Select commit
Hold shift + click to select a range
f0452d4

fix var colorbar labels


melonora Mar 31, 2024
6f63830

fix var plotting in case of vector length 3/4


melonora Apr 1, 2024
9445e36

fix tests


melonora Apr 1, 2024
3d68be0

address comments


melonora Apr 4, 2024
5793bf2

remove unnecessary check


melonora Apr 4, 2024
c33f84a

more informative name


melonora Apr 4, 2024
56ed753

fix prettier


melonora Apr 4, 2024
46448b9

Merge branch 'main' into fix_var_plotting


melonora Apr 4, 2024

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2 changes: 1 addition & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

Expand Down

21 changes: 10 additions & 11 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
 na_color=render_params.cmap_params.na_color,
 )

 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)

 # Then overlay the contour
 labels_contour = _map_color_seg(
 seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
 alpha=render_params.outline_alpha,
 origin="lower",
 )
 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 else:
 # Default: no alpha, contour = infill
 label = _map_color_seg(
Expand Down

25 changes: 19 additions & 6 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

 try:
 # fails when numeric
 fill_c = ColorConverter().to_rgba_array(c)
 if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
 if norm is None:
 c = cmap(c)
 else:
 try:
 norm = colors.Normalize(vmin=min(c), vmax=max(c))
 except ValueError as e:
 raise ValueError(
 "Could not convert values in the `color` column to float, if `color` column represents"
 " categories, set the column to categorical dtype."
 ) from e
 c = cmap(norm(c))
 else:
 fill_c = ColorConverter().to_rgba_array(c)
 except ValueError:
 if norm is None:
 c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
 ax: Axes,
 cax: PatchCollection,
 fig_params: FigParams,
 value_to_plot: str | None, # str | None,
 value_to_plot: str | None,
 color_source_vector: pd.Series[CategoricalDtype],
 adata: AnnData | None = None,
 palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
 params.col_for_color.append(col_color)
 element_table_mapping[element_name] = set()
 else:
 if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
 for table_name in mapping.copy():
 if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
 for table_name in table_set.copy():
 if (
 col_color not in sdata[table_name].obs.columns
 and col_color not in sdata[table_name].var_names
 ):
mapping.remove(table_name)
table_set.remove(table_name)
 params.col_for_color.append(None)
 else:
 params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
 """Force mypy to recognize list of string and None."""
 if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
 checked_parameter = parameter if isinstance(parameter, list) else [None]
 checked_parameter = parameter
 else:
 checked_parameter = [None]
 return checked_parameter
Expand Down

, '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
Fix var plotting#236

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 Merged

melonora
merged 8 commits into

from

Apr 4, 2024
 Merged


Fix var plotting
#236
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f0452d4

fix var colorbar labels


melonora Mar 31, 2024
6f63830

fix var plotting in case of vector length 3/4


melonora Apr 1, 2024
9445e36

fix tests


melonora Apr 1, 2024
3d68be0

address comments


melonora Apr 4, 2024
5793bf2

remove unnecessary check


melonora Apr 4, 2024
c33f84a

more informative name


melonora Apr 4, 2024
56ed753

fix prettier


melonora Apr 4, 2024
46448b9

Merge branch 'main' into fix_var_plotting


melonora Apr 4, 2024

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2 changes: 1 addition & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

Expand Down

21 changes: 10 additions & 11 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
 na_color=render_params.cmap_params.na_color,
 )

 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)

 # Then overlay the contour
 labels_contour = _map_color_seg(
 seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
 alpha=render_params.outline_alpha,
 origin="lower",
 )
 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 else:
 # Default: no alpha, contour = infill
 label = _map_color_seg(
Expand Down

25 changes: 19 additions & 6 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

 try:
 # fails when numeric
 fill_c = ColorConverter().to_rgba_array(c)
 if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
 if norm is None:
 c = cmap(c)
 else:
 try:
 norm = colors.Normalize(vmin=min(c), vmax=max(c))
 except ValueError as e:
 raise ValueError(
 "Could not convert values in the `color` column to float, if `color` column represents"
 " categories, set the column to categorical dtype."
 ) from e
 c = cmap(norm(c))
 else:
 fill_c = ColorConverter().to_rgba_array(c)
 except ValueError:
 if norm is None:
 c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
 ax: Axes,
 cax: PatchCollection,
 fig_params: FigParams,
 value_to_plot: str | None, # str | None,
 value_to_plot: str | None,
 color_source_vector: pd.Series[CategoricalDtype],
 adata: AnnData | None = None,
 palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
 params.col_for_color.append(col_color)
 element_table_mapping[element_name] = set()
 else:
 if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
 for table_name in mapping.copy():
 if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
 for table_name in table_set.copy():
 if (
 col_color not in sdata[table_name].obs.columns
 and col_color not in sdata[table_name].var_names
 ):
mapping.remove(table_name)
table_set.remove(table_name)
 params.col_for_color.append(None)
 else:
 params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
 """Force mypy to recognize list of string and None."""
 if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
 checked_parameter = parameter if isinstance(parameter, list) else [None]
 checked_parameter = parameter
 else:
 checked_parameter = [None]
 return checked_parameter
Expand Down

, '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
Fix var plotting#236

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

melonora
merged 8 commits into

from

Apr 4, 2024
 Merged


Fix var plotting
#236
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f0452d4

fix var colorbar labels


melonora Mar 31, 2024
6f63830

fix var plotting in case of vector length 3/4


melonora Apr 1, 2024
9445e36

fix tests


melonora Apr 1, 2024
3d68be0

address comments


melonora Apr 4, 2024
5793bf2

remove unnecessary check


melonora Apr 4, 2024
c33f84a

more informative name


melonora Apr 4, 2024
56ed753

fix prettier


melonora Apr 4, 2024
46448b9

Merge branch 'main' into fix_var_plotting


melonora Apr 4, 2024

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2 changes: 1 addition & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

Expand Down

21 changes: 10 additions & 11 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
 na_color=render_params.cmap_params.na_color,
 )

 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)

 # Then overlay the contour
 labels_contour = _map_color_seg(
 seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
 alpha=render_params.outline_alpha,
 origin="lower",
 )
 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 else:
 # Default: no alpha, contour = infill
 label = _map_color_seg(
Expand Down

25 changes: 19 additions & 6 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

 try:
 # fails when numeric
 fill_c = ColorConverter().to_rgba_array(c)
 if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
 if norm is None:
 c = cmap(c)
 else:
 try:
 norm = colors.Normalize(vmin=min(c), vmax=max(c))
 except ValueError as e:
 raise ValueError(
 "Could not convert values in the `color` column to float, if `color` column represents"
 " categories, set the column to categorical dtype."
 ) from e
 c = cmap(norm(c))
 else:
 fill_c = ColorConverter().to_rgba_array(c)
 except ValueError:
 if norm is None:
 c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
 ax: Axes,
 cax: PatchCollection,
 fig_params: FigParams,
 value_to_plot: str | None, # str | None,
 value_to_plot: str | None,
 color_source_vector: pd.Series[CategoricalDtype],
 adata: AnnData | None = None,
 palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
 params.col_for_color.append(col_color)
 element_table_mapping[element_name] = set()
 else:
 if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
 for table_name in mapping.copy():
 if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
 for table_name in table_set.copy():
 if (
 col_color not in sdata[table_name].obs.columns
 and col_color not in sdata[table_name].var_names
 ):
mapping.remove(table_name)
table_set.remove(table_name)
 params.col_for_color.append(None)
 else:
 params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
 """Force mypy to recognize list of string and None."""
 if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
 checked_parameter = parameter if isinstance(parameter, list) else [None]
 checked_parameter = parameter
 else:
 checked_parameter = [None]
 return checked_parameter
Expand Down

, '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('^' + ".*" + '

Skip to content
Fix var plotting#236

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Apr 4, 2024
 Merged


Fix var plotting
#236
Show file tree
Hide file tree
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Commits

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8 commits


Select commit
Hold shift + click to select a range
f0452d4

fix var colorbar labels


melonora Mar 31, 2024
6f63830

fix var plotting in case of vector length 3/4


melonora Apr 1, 2024
9445e36

fix tests


melonora Apr 1, 2024
3d68be0

address comments


melonora Apr 4, 2024
5793bf2

remove unnecessary check


melonora Apr 4, 2024
c33f84a

more informative name


melonora Apr 4, 2024
56ed753

fix prettier


melonora Apr 4, 2024
46448b9

Merge branch 'main' into fix_var_plotting


melonora Apr 4, 2024

File filter

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Filter by extension
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2 changes: 1 addition & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

Expand Down

21 changes: 10 additions & 11 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
 na_color=render_params.cmap_params.na_color,
 )

 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)

 # Then overlay the contour
 labels_contour = _map_color_seg(
 seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
 alpha=render_params.outline_alpha,
 origin="lower",
 )
 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 else:
 # Default: no alpha, contour = infill
 label = _map_color_seg(
Expand Down

25 changes: 19 additions & 6 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

 try:
 # fails when numeric
 fill_c = ColorConverter().to_rgba_array(c)
 if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
 if norm is None:
 c = cmap(c)
 else:
 try:
 norm = colors.Normalize(vmin=min(c), vmax=max(c))
 except ValueError as e:
 raise ValueError(
 "Could not convert values in the `color` column to float, if `color` column represents"
 " categories, set the column to categorical dtype."
 ) from e
 c = cmap(norm(c))
 else:
 fill_c = ColorConverter().to_rgba_array(c)
 except ValueError:
 if norm is None:
 c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
 ax: Axes,
 cax: PatchCollection,
 fig_params: FigParams,
 value_to_plot: str | None, # str | None,
 value_to_plot: str | None,
 color_source_vector: pd.Series[CategoricalDtype],
 adata: AnnData | None = None,
 palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
 params.col_for_color.append(col_color)
 element_table_mapping[element_name] = set()
 else:
 if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
 for table_name in mapping.copy():
 if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
 for table_name in table_set.copy():
 if (
 col_color not in sdata[table_name].obs.columns
 and col_color not in sdata[table_name].var_names
 ):
mapping.remove(table_name)
table_set.remove(table_name)
 params.col_for_color.append(None)
 else:
 params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
 """Force mypy to recognize list of string and None."""
 if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
 checked_parameter = parameter if isinstance(parameter, list) else [None]
 checked_parameter = parameter
 else:
 checked_parameter = [None]
 return checked_parameter
Expand Down

, '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); }
})();
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Fix var plotting#236

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 Merged

melonora
merged 8 commits into

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Apr 4, 2024
 Merged


Fix var plotting
#236
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f0452d4

fix var colorbar labels


melonora Mar 31, 2024
6f63830

fix var plotting in case of vector length 3/4


melonora Apr 1, 2024
9445e36

fix tests


melonora Apr 1, 2024
3d68be0

address comments


melonora Apr 4, 2024
5793bf2

remove unnecessary check


melonora Apr 4, 2024
c33f84a

more informative name


melonora Apr 4, 2024
56ed753

fix prettier


melonora Apr 4, 2024
46448b9

Merge branch 'main' into fix_var_plotting


melonora Apr 4, 2024

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2 changes: 1 addition & 1 deletion
CHANGELOG.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning][].

### Fixed

- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap
- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap

## [0.2.0] - 2024-03-24

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21 changes: 10 additions & 11 deletions
src/spatialdata_plot/pl/render.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -677,17 +677,6 @@ def _render_labels(
 na_color=render_params.cmap_params.na_color,
 )

 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)

 # Then overlay the contour
 labels_contour = _map_color_seg(
 seg=label.values,
Expand All@@ -708,6 +697,16 @@ def _render_labels(
 alpha=render_params.outline_alpha,
 origin="lower",
 )
 _cax = ax.imshow(
 labels_infill,
 rasterized=True,
 cmap=None if categorical else render_params.cmap_params.cmap,
 norm=None if categorical else render_params.cmap_params.norm,
 alpha=render_params.fill_alpha,
 origin="lower",
 )
 _cax.set_transform(trans_data)
 cax = ax.add_image(_cax)
 else:
 # Default: no alpha, contour = infill
 label = _map_color_seg(
Expand Down

25 changes: 19 additions & 6 deletions
src/spatialdata_plot/pl/utils.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -206,7 +206,20 @@ def _get_collection_shape(

 try:
 # fails when numeric
 fill_c = ColorConverter().to_rgba_array(c)
 if len(c.shape) == 1 and c.shape[0] in [3, 4] and c.shape[0] == len(shapes) and c.dtype == float:
 if norm is None:
 c = cmap(c)
 else:
 try:
 norm = colors.Normalize(vmin=min(c), vmax=max(c))
 except ValueError as e:
 raise ValueError(
 "Could not convert values in the `color` column to float, if `color` column represents"
 " categories, set the column to categorical dtype."
 ) from e
 c = cmap(norm(c))
 else:
 fill_c = ColorConverter().to_rgba_array(c)
 except ValueError:
 if norm is None:
 c = cmap(c)
Expand DownExpand Up@@ -826,7 +839,7 @@ def _decorate_axs(
 ax: Axes,
 cax: PatchCollection,
 fig_params: FigParams,
 value_to_plot: str | None, # str | None,
 value_to_plot: str | None,
 color_source_vector: pd.Series[CategoricalDtype],
 adata: AnnData | None = None,
 palette: ListedColormap | str | list[str] | None = None,
Expand DownExpand Up@@ -1465,13 +1478,13 @@ def _validate_colors_element_table_mapping_points_shapes(
 params.col_for_color.append(col_color)
 element_table_mapping[element_name] = set()
 else:
 if isinstance(mapping := element_table_mapping[element_name], set) and len(mapping.copy()) != 0:
 for table_name in mapping.copy():
 if isinstance(table_set := element_table_mapping[element_name], set) and len(table_set) != 0:
 for table_name in table_set.copy():
 if (
 col_color not in sdata[table_name].obs.columns
 and col_color not in sdata[table_name].var_names
 ):
mapping.remove(table_name)
table_set.remove(table_name)
 params.col_for_color.append(None)
 else:
 params.col_for_color.append(col_color)
Expand DownExpand Up@@ -1957,7 +1970,7 @@ def _is_coercable_to_float(series: pd.Series) -> bool:
def _return_list_str_none(parameter: list[str | None] | str | None) -> list[str | None]:
 """Force mypy to recognize list of string and None."""
 if isinstance(parameter, list) and all(isinstance(item, (str, type(None))) for item in parameter):
 checked_parameter = parameter if isinstance(parameter, list) else [None]
 checked_parameter = parameter
 else:
 checked_parameter = [None]
 return checked_parameter
Expand Down