MatplotlibDeprecationWarning: "You are modifying the state of a globally registered colormap." #995
Description
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Search whether this issue (or a similar issue) has been solved before
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Paste your deepTools version (
deeptools --version) and your python
version (python --version) below.
deeptools 3.4.3Python 3.7.1
- Paste the full deepTools command that produces the issue below
(ignore if you simply spotted the issue in the code/documentation).
plotHeatmap \
--matrixFile /home/analysis/projects/tnfalpha/results/matrix/custom_normalization/MED1_tnfa-MED1_ctrl/computeMatrix.mat.gz \
--outFileName /home/analysis/projects/tnfalpha/plots/heatmaps/custom_normalization/MED1_tnfa-MED1_ctrl/heatmap.svg \
--whatToShow 'plot, heatmap and colorbar' \
--refPointLabel 'Peak center' \
--samplesLabel MED1_TNF_1 MED1_TNF_2 MED1_Veh_1 MED1_Veh_2_1 MED1_Veh_2_2 Input_TNF Input_Veh \
--regionsLabel 'up-regulated peaks (1069)' 'non-regulated peaks (16034)' 'down-regulated peaks (289)' \
--colorMap Reds Reds Blues Blues Blues Greys Greys \
--legendLocation best \
--zMin 0 \
--zMax 93.64 \
--heatmapWidth 6
- Paste the output printed on screen from the command that produces the issue
below (ignore if you simply spotted the issue in the code/documentation).
/home/miniconda3/lib/python3.7/site-packages/deeptools/plotHeatmap.py:454: MatplotlibDeprecationWarning:
You are modifying the state of a globally registered colormap. In future versions, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = copy.copy(mpl.cm.get_cmap("Reds"))
/home/miniconda3/lib/python3.7/site-packages/deeptools/plotHeatmap.py:454: MatplotlibDeprecationWarning:
You are modifying the state of a globally registered colormap. In future versions, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = copy.copy(mpl.cm.get_cmap("Blues"))
/home/miniconda3/lib/python3.7/site-packages/deeptools/plotHeatmap.py:454: MatplotlibDeprecationWarning:
You are modifying the state of a globally registered colormap. In future versions, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = copy.copy(mpl.cm.get_cmap("Greys"))
/home/miniconda3/lib/python3.7/site-packages/deeptools/plotHeatmap.py:711: MatplotlibDeprecationWarning:
The 'alpha' parameter to Colorbar has no effect because it is overridden by the mappable; it is deprecated since 3.3 and will be removed two minor releases later.
/home/miniconda3/lib/python3.7/site-packages/deeptools/plotHeatmap.py:743: MatplotlibDeprecationWarning:
savefig() got unexpected keyword argument "pdd_inches" which is no longer supported as of 3.3 and will become an error two minor releases later
Hey! It seems like there have been some changes within Matplotlib that cause this warning. I haven't found an issue (open or closed) and the release notes for 3.5.0 don't seem to indicate that this has been addressed.