Error with plot-related functions when running pycisTopic

[zhli12]

Hello,

I'm having some troubles using plotting functions in pycisTopic when runnign the tutorial [(https://pycistopic.readthedocs.io/en/latest/notebooks/human_cerebellum.html#Run-models)], including plot_metadata, plot_topic, and cell_topic_heatmap.

plot_metadata and plot_topic give the error

ValueError: Unable to determine Axes to steal space for Colorbar. Either provide the *cax* argument to use as the Axes for the Colorbar, provide the *ax* argument to steal space from it, or add *mappable* to an Axes.

while cell_topic_heatmap gives the error

KeyError: "None of [Index(['TGACTCCTCATCCACC-1-10x_multiome_brain',\n 'TTTCTCACATAAACCT-1-10x_multiome_brain',\n 'GTCCTCCCACACAATT-1-10x_multiome_brain',\n 'ACATAGCTCATTAGTG-1-10x_multiome_brain',\n 'GACCTAAGTTTGGCGG-1-10x_multiome_brain',\n 'TGTGTTAAGGCCTAAT-1-10x_multiome_brain',\n 'AGGAACGGTTCGCTCA-1-10x_multiome_brain',\n 'TTTCTCACAATAATGG-1-10x_multiome_brain',\n 'TTAACTGAGGATCACT-1-10x_multiome_brain',\n 'GTACTAATCGCAGGCT-1-10x_multiome_brain',\n ...\n 'CGGTTGGGTTATCCTA-1-10x_multiome_brain',\n 'AGCTAAACACCTACGG-1-10x_multiome_brain',\n 'CCATCACTCTCTAGCC-1-10x_multiome_brain',\n 'TACTGGCCACCGGTAT-1-10x_multiome_brain',\n 'CTTAAGGGTGTTAGCA-1-10x_multiome_brain',\n 'GGCTCACAGGCCCAGT-1-10x_multiome_brain',\n 'GTAGTTATCATAAGCC-1-10x_multiome_brain',\n 'CAGAATCTCCTCATGC-1-10x_multiome_brain',\n 'TAGCCGGGTAACAGGG-1-10x_multiome_brain',\n 'GTGCGCAGTGCTTAGA-1-10x_multiome_brain'],\n dtype='object', length=1575)] are in the [columns]"

I found some related posts (#247 and #501) but the errors seem to be unsolved yet, so I'm wondering whether anyone has some idea about this. Thanks!

Below is the pacakge versions I used:

System Information:
OS: Linux 4.15.0-213-generic
Python Version: 3.11.10 | packaged by conda-forge | (main, Oct 16 2024, 01:27:36) [GCC 13.3.0]
==================================================
Installed Packages and Versions:
Package                              Version
------------------------------------ -----------------
adjustText                           1.0.4
aiohappyeyeballs                     2.4.3
aiohttp                              3.9.3
aiohttp-cors                         0.7.0
aiosignal                            1.3.1
anndata                              0.10.5.post1
annotated-types                      0.7.0
annoy                                1.17.3
ansicolors                           1.1.8
anyio                                4.6.2.post1
appdirs                              1.4.4
arboreto                             0.1.6
argon2-cffi                          23.1.0
argon2-cffi-bindings                 21.2.0
argparse-dataclass                   2.0.0
array_api_compat                     1.5.1
arrow                                1.3.0
asttokens                            2.4.1
async-lru                            2.0.4
attr                                 0.3.2
attrs                                23.2.0
babel                                2.16.0
bbknn                                1.6.0
beautifulsoup4                       4.12.3
bidict                               0.23.1
bioservices                          1.11.2
bleach                               6.2.0
blessed                              1.20.0
blosc2                               2.5.1
bokeh                                3.4.0
boltons                              23.1.1
Brotli                               1.1.0
bs4                                  0.0.2
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cachetools                           5.5.0
cattrs                               23.2.3
certifi                              2024.2.2
cffi                                 1.17.1
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MACS2                                2.2.9.1
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marshmallow                          3.21.1
matplotlib                           3.6.3
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mistune                              3.0.2
mizani                               0.9.3
msgpack                              1.0.8
mudata                               0.2.3
multidict                            6.0.5
multiprocessing-on-dill              3.5.0a4
munkres                              1.1.4
mypy-extensions                      1.0.0
natsort                              8.4.0
nbclient                             0.10.0
nbconvert                            7.16.4
nbformat                             5.10.3
nbsphinx                             0.9.5
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ncls                                 0.0.68
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protobuf                             5.26.0
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py-cpuinfo                           9.0.0
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pycistarget                          1.0a2
pycisTopic                           2.0a0
pycparser                            2.22
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pydantic_core                        2.23.4
pyfasta                              0.5.2
pygam                                0.9.0
Pygments                             2.17.2
pynndescent                          0.5.11
pyOpenSSL                            24.2.1
pyparsing                            3.1.2
pyranges                             0.0.111
pyrle                                0.0.39
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pyscenic                             0.12.1+8.gd2309fe
PySide6                              6.8.0.2
PySocks                              1.7.1
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[genomic-coder]

Hello, could you find a resolution or did you just go ahead without this step?

[SeppeDeWinter]

Hi

This error is related to your matplotlib version.
matplotlib/matplotlib#23973

Best,

S

[zhli12]

Thanks! The problem is indeed related to matplotlib version and is solved now.

[YushaLiu]

Hi @zhli12, I got the same error as you when running cell_topic_heatmap. Could you share in more detail how you finally solved this error? Did you downgrade matplotlib? If so, to which version? Thanks very much!

[YushaLiu]

@SeppeDeWinter @zhli12 Is the error from calling cell_topic_heatmap (i.e., none of [Index(...)] are in the [columns], which was also reported in #501) caused by the transpose operation in line 934 in clust_vis.py, such that the barcodes in the transposed cell_data are in rows rather than columns? This seems to have nothing to do with the version of the matplotlib package... Is this a bug that needs to be fixed?

[zhli12]

Hi @zhli12, I got the same error as you when running cell_topic_heatmap. Could you share in more detail how you finally solved this error? Did you downgrade matplotlib? If so, to which version? Thanks very much!

The matplotlib version I'm using now is 3.6.3. It fixed You are right that this doesn't fix the error in cell_topic_heatmap.

Hi @zhli12, I got the same error as you when running cell_topic_heatmap. Could you share in more detail how you finally solved this error? Did you downgrade matplotlib? If so, to which version? Thanks very much!

hmm You are right. After changing the versions I got rid of the errors from running plot_metadata and plot_topic but I still couldn't run cell_topic_heatmap.