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heatmap cluster-color bar #521

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ShobiStassen opened this issue Mar 8, 2019 · 2 comments
Closed

heatmap cluster-color bar #521

ShobiStassen opened this issue Mar 8, 2019 · 2 comments

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@ShobiStassen
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Hi,
I would like to set the scatterplot color palette and the heatmap cluster-color bar palette to be the same so that the clusters in the scatterplot are the same as those in the heatmap cluster-color-bar. I am using matplotlib to plot a scatterplot (using some other embedding) and need the cluster colors to match those in the automatic colorbar on the heatmap clusterbar.
If i globally set the palette using sc.set_figure_params() then the values of the heatmap plot also become the global cmap (rather than a gradient of red-blue or existing default)
Thanks for your help
Shobi

@fidelram
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fidelram commented Mar 8, 2019

In principle the scatter plot and the the heatmap use the same colors. See for example: https://scanpy-tutorials.readthedocs.io/en/latest/visualizing-marker-genes.html#Heatmaps

The colors on the left are the same colors stored for the scatter plot clusters.

@ivirshup
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If the issue is continuous color maps, that can be specified with the cmap parameter.

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