cbScanpy dies on PAGA about cellbrowser HOT 9 CLOSED

I then tried a run with this:
doLayouts = ['umap', 'phate', 'fa', 'fr', 'grid_fr', 'kk', 'lgl', 'drl', 'rt']
and that died with

ERROR:root:layout name grid_fr is not valid. Valid layouts: {'fa': 'ForceAtlas2', 'fr': 'Fruchterman Reingold', 'kk': 'Kamadi Kawai', 'drl': 'DrL Distributed Recursive Layout', 'tsne': 't-SNE', 'umap': 'UMAP', 'pagaFa': 'PAGA/ForceAtlas2', 'pagaFr': 'PAGA/Fruchterman-Reingold', 'phate': 'PHATE'}

Note that lgl and rt are also not listed as a valid layout, though they are listed as 'possible options' in scanpy.conf

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I'm leaving this open for now until I hear back from you.

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BTW I've successfully run cbScanpy using doLayouts="all" right now on pbmc_small

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from cellbrowser.

cbScanpy apparently worked for you now.

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Looks like I can't reopen this issue, but I just pip installed 0.4.24 and still get

Performing PAGA+ForceAtlas2
Traceback (most recent call last):
  File "/home/cellranger/anaconda3/envs/cellBrowserConda/bin/cbScanpy", line 11, in <module>
    sys.exit(cbScanpyCli())
  File "/home/cellranger/anaconda3/envs/cellBrowserConda/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 3435, in cbScanpyCli
    adata = cbScanpy(matrixFname, confFname, figDir, logFname)
  File "/home/cellranger/anaconda3/envs/cellBrowserConda/lib/python3.6/site-packages/cellbrowser/cellbrowser.py", line 3341, in cbScanpy
    adata.obsm["X_pagaFa"] = adata.obsm["X_draw_graph_fa"]
  File "/home/cellranger/anaconda3/envs/cellBrowserConda/lib/python3.6/site-packages/numpy/core/records.py", line 500, in __getitem__
    obj = super(recarray, self).__getitem__(indx)
ValueError: no field of name X_draw_graph_fa

This happens with scanpy 1.3.2 and also after pip --upgrade scanpy with 1.3.6

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Yes cbScanpy and yes "all".
To get it to work I replaced the recommendedLayouts line in cellbrowser.py with one that excludes PAGA and then it runs.
This is the full list of dependencies as printed at the top of the log:
scanpy==1.3.6 anndata==0.6.15 numpy==1.14.0 scipy==1.1.0 pandas==0.23.4 scikit-learn==0.20.0 statsmodels==0.9.0 python-igraph==0.7.1 louvain==0.6.1

I did pip --upgrade on all of these and ran with doLayouts=["pagaFa"]. Same error.
scanpy==1.3.6 anndata==0.6.15 numpy==1.15.4 scipy==1.1.0 pandas==0.23.4 scikit-learn==0.20.1 statsmodels==0.9.0 python-igraph==0.7.1 louvain==0.6.1

Note that the actual error comes from numpy/core/records.py so I thought the upgrade would help...

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