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Update MARK to include pts, pts_rest keys in marker gene table #81

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Update MARK to include pts, pts_rest keys in marker gene table #81

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5ef29f4
Updated MARK to include pts, pts_rest keys in table for fraction of c…
sylviamic Sep 19, 2022
1be435b
Corrected logic for using minimum 2 groups in MARK function. Updated …
sylviamic Sep 20, 2022
1f70839
Merge branch 'interactivereport:master' into master
sylviamic Apr 12, 2023
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14 changes: 8 additions & 6 deletions VIPInterface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1139,21 +1139,21 @@ def MARK(data):
keepG = [key for key,val in vCount.items() if val>2]
adata = adata[adata.obs[data["grp"][0]].isin(keepG),:]

if len(adata.obs[data['grp'][0]].unique())<3:
return 'ERROR @server: {}'.format('Less than 3 groups in selected cells! Please use DEG for 2 groups')
if (len(adata.obs[data['grp'][0]].unique())<2) and (data['markMethod']=="logreg"):
return 'ERROR @server: {}'.format('Less than 2 groups in selected cells! Please select a different method or use the DEG interface for 2 groups')
#return json.dumps([[['name','scores'],['None','0']],Msg('Less than 3 groups in selected cells!Please use DEG for 2 groups')])

sc.tl.rank_genes_groups(adata,groupby=data["grp"][0],n_genes=int(data['geneN']),method=data['markMethod'])#
sc.tl.rank_genes_groups(adata,groupby=data["grp"][0],n_genes=int(data['geneN']),method=data['markMethod'],pts=True)#
ppr.pprint(int(data['geneN']))
sc.pl.rank_genes_groups(adata,n_genes=int(data['geneN']),ncols=min([3,len(adata.obs[data['grp'][0]].unique())]),show=False)
fig =plt.gcf()

gScore = adata.uns['rank_genes_groups']
#ppr.pprint(gScore)
pKeys = [i for i in ['names','scores','logfoldchanges','pvals','pvals_adj'] if i in gScore.keys()]
pKeys = [i for i in ['names','scores','logfoldchanges','pvals','pvals_adj','pts','pts_rest'] if i in gScore.keys()]
scoreM = [pKeys+['Group']]
for i in gScore['scores'].dtype.names:
for j in range(len(gScore['scores'][i])):
for i in gScore['scores'].dtype.names: # iterate over groups
for j in range(len(gScore['scores'][i])): # iterate over gene index (int)
one = []
for k in pKeys:
if k=='logfoldchanges':
Expand All @@ -1162,6 +1162,8 @@ def MARK(data):
one += ['%.4E' % gScore[k][i][j]]
elif k=='scores':
one += ['%.4f' % gScore[k][i][j]]
elif k in ['pts', 'pts_rest']:
one += ['%.2f' % gScore[k].at[gScore['names'][i][j], i]]
else:
one += [gScore[k][i][j]]
scoreM += [one+[i]]
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