making cbscanpy output the raw and full expression matrix, not the fi…

…ltered one.
ucscGenomeBrowser · Dec 7, 2018 · bba1be0 · bba1be0
1 parent 0c85a79
commit bba1be0
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/sampleData/pbmc_small/scanpy.conf b/sampleData/pbmc_small/scanpy.conf
@@ -55,7 +55,8 @@ louvainRes = 1.0
 #     Tilford tree layout).
 # You can also set doLayouts="all" to generate all possible layouts mentioned above.
 #doLayouts = ["fa", "umap"]
-doLayouts = "all"
+#doLayouts = "all"
+doLayouts = ["umap", "pagaFa", "fa", "fr", "kk", "lgl", "drl", "rt"]
 
 # find top marker genes per cluster?
 doMarkers = True

diff --git a/src/cbPyLib/cellbrowser/cellbrowser.py b/src/cbPyLib/cellbrowser/cellbrowser.py
@@ -2637,7 +2637,11 @@ def anndataToTsv(ad, matFname, usePandas=False):
             ofh.write("\n")
 
         ofh.close()
-    os.rename(tmpFname, matFname)
+
+    if matFname.endswith(".gz"):
+        runGzip(tmpFname, matFname)
+    else:
+        os.rename(tmpFname, matFname)
 
 def makeDictDefaults(inVar, defaults):
     " convert inVar to dict if necessary, defaulting to our default labels "
@@ -2683,9 +2687,8 @@ def scanpyToCellbrowser(adata, path, datasetName, metaFields=["louvain", "percen
     import anndata
 
     if not skipMatrix:
-        matFname = join(path, 'exprMatrix.tsv')
+        matFname = join(path, 'exprMatrix.tsv.gz')
         anndataToTsv(adata, matFname)
-        matFname = runGzip(matFname)
 
     if coordFields=="all" or coordFields is None:
         coordFields = coordLabels