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Improve consistency in color file export and simplify marker gene fallback logic #9

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Improve consistency in color file export and simplify marker gene fallback logic #9

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47b3e66
fix: standardize color file path handling in scanpy export
sposadac Jun 17, 2025
f42bb71
fix: simplify fallback logic for marker gene computation
sposadac Jun 17, 2025
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28 changes: 12 additions & 16 deletions src/cbPyLib/cellbrowser/cellbrowser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5210,9 +5210,9 @@ def check_nonnegative_integers(X):

def exportScanpyOneFieldColor(fieldName, fieldValues, colors, outDir, configData):
"write a single color file, for one field"
outFname = join(outDir, fieldName+"_colors.tsv")
outFname = join(outDir, fieldName + "_colors.tsv")
logging.info("Writing colors of field %s to %s" % (fieldName, outFname))

# Debugging: print lengths and contents
#print(f"Field name: {fieldName}")
#print(f"Field values (length {len(fieldValues)}): {fieldValues}")
Expand All @@ -5224,28 +5224,24 @@ def exportScanpyOneFieldColor(fieldName, fieldValues, colors, outDir, configData
# Handle mismatch: you can either raise an exception or handle it gracefully
return

ofh = open(outFname, "w")
ofh.write("#val color\n")
for val, color in zip(fieldValues, colors):
ofh.write("%s\t%s\n" % (val, color))
ofh.close()
with open(outFname, "w") as ofh:
ofh.write("#val\tcolor\n")
for val, color in zip(fieldValues, colors):
ofh.write("%s\t%s\n" % (val, color))

if "colors" not in configData:
configData["colors"] = {}
configData["colors"][fieldName] = outFname
configData["colors"][fieldName] = fieldName + "_colors.tsv"

def exportScanpyColors(adata, outDir, configData):
" create one tsv with the colors per color definition in adata "
for fieldName in adata.obs.keys():
colorKey = fieldName+"_colors"
#if colorKey in adata.uns:
#outFname = exportScanpyOneFieldColor(fieldName, adata.obs[fieldName].values.categories, adata.uns[colorKey], outDir, configData)
colorKey = fieldName + "_colors"
if colorKey in adata.uns and adata.uns[colorKey] is not None and len(adata.uns[colorKey]) > 0:
fieldValues = adata.obs[fieldName].values.categories
colors = adata.uns[colorKey]
# Check if colors is a list/array and has a non-zero length
colors = adata.uns[colorKey]
if colors is not None and len(colors) > 0:
fieldValues = adata.obs[fieldName].values.categories
outFname = exportScanpyOneFieldColor(fieldName, fieldValues, colors, outDir, configData)
exportScanpyOneFieldColor(fieldName, fieldValues, colors, outDir, configData)
else:
logging.warning("Skipping %s because colors are not available or empty." % fieldName)
return configData
Expand Down Expand Up @@ -5339,7 +5335,7 @@ def scanpyToCellbrowser(adata, path, datasetName, metaFields=None, clusterField=
logging.warn("No valid embeddings were found in anndata.obsm but at least one array of coordinates is usually required. Keys obsm: %s" % (coordFields))

##Check for cluster markers
if (markerField not in adata.uns or clusterField is not None) and not skipMarkers:
if markerField not in adata.uns and not skipMarkers:
logging.warn("Couldnt find list of cluster marker genes in the h5ad file in adata.uns with the key '%s'. "
"In the future, from Python, try running sc.tl.rank_genes_groups(adata) to "
"create the cluster annotation and write the h5ad file then." % markerField)
Expand Down