Merge pull request #8 from asrhou/master

fixed many bugs
asrhou · Aug 19, 2020 · 6c1275f · 6c1275f
2 parents ae7a593 + f8ecc9a
commit 6c1275f
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Showing 2 changed files with 25 additions and 5 deletions.
diff --git a/DiffEdges.py b/DiffEdges.py
@@ -48,6 +48,20 @@ def IdentifyPopulationChanges(refClusterMapDF, testClusterMapDF, resultFolder, r
 
     sumClusterDF = pd.concat([refClusterSizeDF, testClusterSizeDF])
     sumClusterDF.columns = ['Cluster', 'Population (cells)', 'Fraction (%)', 'Source']
+    newsumClusterDFDict = {'Cluster':[], 'Population (cells)':[], 'Fraction (%)':[], 'Source':[]}
+    for cct in set(sumClusterDF['Cluster']):
+        tsumClusterDF = sumClusterDF.loc[sumClusterDF['Cluster']==cct,]
+        if len(tsumClusterDF) == 1:
+            sourcetype = tsumClusterDF.loc[tsumClusterDF.index[0],'Source']
+            newsumClusterDFDict['Cluster'].append(cct)
+            newsumClusterDFDict['Population (cells)'].append(0)
+            newsumClusterDFDict['Fraction (%)'].append(0.0)
+            if sourcetype == 'reference dataset':
+                newsumClusterDFDict['Source'].append('target dataset')
+            else:
+                newsumClusterDFDict['Source'].append('reference dataset')
+    newsumClusterDF = pd.DataFrame(newsumClusterDFDict)
+    sumClusterDF = pd.concat([sumClusterDF, newsumClusterDF])
     sumClusterDF = sumClusterDF.sort_values(by=['Cluster'])
     sumClusterDF.set_index('Cluster').to_excel(os.path.join(resultFolder,'cluster_comparison.xlsx'), index=True, header=True)
 
@@ -73,11 +87,11 @@ def IdentifyPopulationChanges(refClusterMapDF, testClusterMapDF, resultFolder, r
     # visualise population changes in clusters
     sns.set_style("whitegrid")
     fig = plt.figure(figsize=(plotWidth, plotHeight))
-    ax = sns.barplot(y="Cluster", x="Population (cells)", hue="Source", data=sumClusterDF, order=cltOrder, palette={'reference dataset':'r','target dataset':'lime'})
+    ax = sns.barplot(y="Cluster", x="Population (cells)", hue="Source", data=sumClusterDF, order=cltOrder, palette={'reference dataset':'red','target dataset':'blue'})
     fig = ax.get_figure()
     fig.savefig(os.path.join(resultFolder,'cluster_size_comparison.pdf'), bbox_inches='tight')
     fig = plt.figure(figsize=(plotWidth, plotHeight))
-    ax = sns.barplot(y="Cluster", x="Fraction (%)", hue="Source", data=sumClusterDF, order=cltOrder, palette={'reference dataset':'r','target dataset':'lime'})
+    ax = sns.barplot(y="Cluster", x="Fraction (%)", hue="Source", data=sumClusterDF, order=cltOrder, palette={'reference dataset':'red','target dataset':'blue'})
     fig = ax.get_figure()
     fig.savefig(os.path.join(resultFolder,'cluster_fraction_comparison.pdf'), bbox_inches='tight')
 

diff --git a/VisInteractions.py b/VisInteractions.py
@@ -563,6 +563,7 @@ def DrawDeltaGraphvizPlot(readmeStr, typeStr, numStr, nxgS1, adjSpecM1, nxgS2, a
             cltSizeColorDict[clt] = (1,0,0)
         else:
             cltSizeColorDict[clt] = (1, 1, 0)
+
     # draw delta networks
 
     # convert to a graphviz graph
@@ -966,7 +967,9 @@ def DrawGraphvizPlot(readmeStr, typeStr, numStr, nxgS, adjSpecM, dataType, resul
 def BuildDeltaInterClusterNetwork(origlabels, labels, cltSizes, ccolorList, edgeDF, specificityThreshold, weightThreshold, frequencyThreshold, keepTopEdge, interDB, weightType, layout, plotFormat, plotWidth, plotHeight, fontSize, edgeWidth, maxClusterSize, clusterDistance, resultDir, dataType=''):
     readmeStr = '\n'
 
-    compT = pd.read_excel(os.path.join(resultDir,'..','cluster_comparison.xlsx'), index_col=0,header=0)
+    compT = pd.read_excel(os.path.join(resultDir,'..','cluster_comparison.xlsx'), index_col=None,header=0)
+    compT = compT.sort_values(by=['Cluster','Source'])
+    compT = compT.set_index('Cluster')
     cltFDdict = {}
     maxFC = 0
     inflist = []
@@ -980,7 +983,7 @@ def BuildDeltaInterClusterNetwork(origlabels, labels, cltSizes, ccolorList, edge
                 cltFDdict[compT.index[idx]] = 1.0*tempFC
             if maxFC < tempFC:
                 maxFC = tempFC
-        elif compT.iloc[idx,1] == 0:
+        elif compT.iloc[idx,1] * compT.iloc[idx+1,1] == 0:
             inflist.append(idx)
     #set inf as 2 x max fold change
     maxFC = maxFC *2
@@ -1786,7 +1789,8 @@ def DrawTopLRCltPairs(readmeStr, edgeDF, plotFormat,plotWidth, plotHeight, fontS
         topLRE = list(edgeDFE.loc[:,['lrpair']].drop_duplicates().head(10)['lrpair'])
         topLRS = list(edgeDFS.loc[:,['lrpair']].drop_duplicates().head(10)['lrpair'])
     topEdgeDFE = edgeDFE.loc[edgeDFE['lrpair'].isin(topLRE)]
-    topEdgeDFS = edgeDFE.loc[edgeDFS['lrpair'].isin(topLRS)]
+    topEdgeDFS = edgeDFS.loc[edgeDFS['lrpair'].isin(topLRS)]
+
     lrCltMtxE = pd.DataFrame()
     for idx in topEdgeDFE.index:
         if dataType == '':
@@ -1799,6 +1803,7 @@ def DrawTopLRCltPairs(readmeStr, edgeDF, plotFormat,plotWidth, plotHeight, fontS
             lrCltMtxS.loc[topEdgeDFS.loc[idx,'lrpair'],topEdgeDFS.loc[idx,'cellpair']] = topEdgeDFS.loc[idx,'product of specified']
         else:
             lrCltMtxS.loc[topEdgeDFS.loc[idx,'lrpair'],topEdgeDFS.loc[idx,'cellpair']] = topEdgeDFS.loc[idx,'delta specificity']
+
     lrnum = lrCltMtxE.shape[0]
     if lrCltMtxE.shape[0]*2 < lrCltMtxE.shape[1]:
         ctnum = lrnum*2
@@ -1833,6 +1838,7 @@ def DrawTopLRCltPairs(readmeStr, edgeDF, plotFormat,plotWidth, plotHeight, fontS
 
     #draw heatmap
     cmap = 'afmhot_r'
+    #cmap = 'coolwarm'
     import matplotlib.pyplot as plt
     lrCltMtxE = lrCltMtxE.divide(lrCltMtxE.max(axis=1),axis=0)
     f, ax = plt.subplots(figsize=(max(lrCltMtxS.shape),max(lrCltMtxS.shape)/scaleE))