How to set vmax and vmin of cmap in ClusterMapPlotter()
XuejianXiong opened this issue · 7 comments
Good morning,
I would like to set a same range, i.e. vmin and vmax, of cmap in the heatmap for several figures using the function ClusterMapPlotter(). My code is as follows:
heatmap = pch.ClusterMapPlotter(
data=heatmap_data.T,
top_annotation=col_ha,
col_cluster=False,
row_cluster=True,
label="values",
col_dendrogram=False,
row_dendrogram=True,
show_rownames=True,
show_colnames=False,
legend_gap=7,
vmin=0,
vmax=30,
cmap="parula",
rasterized=True,
tree_kws={"row_cmap": "Dark2"},
ylabel=f"Protein (10 in total)",
xlabel=f"Run (100 in total)",
legend_hpad=7,
yticklabels=True,
xticklabels_kws={"labelrotation": -45, "labelcolor": "blue"},
yticklabels_kws={"labelsize": 8},
)
However, the legend in the output figure did not show the range from 0 to 30, but the real minimum and maximum in the heatmap_data.
I would like to know how to solve this problem. Thank you!
Were you using the latest version of PyComplexHeatmap? If not, please upgrade to the latest version. @XuejianXiong
Thank you @DingWB. I upgraded to the version 1.7.3, but still have the same problem.
This is weird; this bug was fixed a long time ago.
Please print print(heatmap.kwargs['vmax'],heatmap.kwargs['vmin'],heatmap.legend_kws) after running heatmap = pch.ClusterMapPlotter(**) and show me the output.
@XuejianXiong
The output looks good "30 0 {'vmin': 0, 'vmax': 30}". However in the figures (attached), it still shows different values in the legend for different heatmaps.
Please install the latest version from github, and follow this example to see whether the legend has the same vmax and vmin as provided in the code (vmin=-2.2,vmax=2.3,).
If it is still not working, then you need to paste your data and code here.
Hi @XuejianXiong ,
How is it going? Did it work?
Hi @DingWB,
It worked! It seems my virtual environment caused issues with the package upgrading. I have to manually delete the old version and reinstall using pip.
Thank you for your help!
Best,
Xuenjian