How to suppress drawing dendrograms but still cluster in seaborn?
Question:
I want to plot a clustermap in seaborn, clustered by both rows and columns. I do not want to draw the dendrograms.
Setting row_cluster=False or col_cluster=False removes the dendrograms, but also stops the clustering.
How do I still 2D cluster but suppress the dendrograms?
This question provides a hack of setting the width of the dendrogram lines to 0. This hack does not work in seaborn 0.7.1.
Answers:
The answer is buried in the documentation.
Let cg be the clustermap instance returned by Seaborn.
After drawing the clustermap, type the following to remove the row dendrogram.
cg.ax_row_dendrogram.set_visible(False)
If you want to preserve the legend, type:
cg.ax_row_dendrogram.set_xlim([0,0])
This is a hack, but set_axis_off() does not seem to do in Seaborn what it does in matplotlib.
To build on the answer by mac389, if you want to suppress the dendrogram in both columns and rows do the following:
cg.ax_row_dendrogram.set_visible(False) #suppress row dendrogram
cg.ax_col_dendrogram.set_visible(False) #suppress column dendrogram
You can also suppress the cbar as indicated by Yacine.
Actually the easiest way to do that would be by using the tree_kwd argument to set the linewidts parameter of the underlying matplotlib.collections.LineCollection object to zero.
clustermap(YOUR_DATA, tree_kws={"linewidths": 0.})
I want to plot a clustermap in seaborn, clustered by both rows and columns. I do not want to draw the dendrograms.
Setting row_cluster=False or col_cluster=False removes the dendrograms, but also stops the clustering.
How do I still 2D cluster but suppress the dendrograms?
This question provides a hack of setting the width of the dendrogram lines to 0. This hack does not work in seaborn 0.7.1.
The answer is buried in the documentation.
Let cg be the clustermap instance returned by Seaborn.
After drawing the clustermap, type the following to remove the row dendrogram.
cg.ax_row_dendrogram.set_visible(False)
If you want to preserve the legend, type:
cg.ax_row_dendrogram.set_xlim([0,0])
This is a hack, but set_axis_off() does not seem to do in Seaborn what it does in matplotlib.
To build on the answer by mac389, if you want to suppress the dendrogram in both columns and rows do the following:
cg.ax_row_dendrogram.set_visible(False) #suppress row dendrogram
cg.ax_col_dendrogram.set_visible(False) #suppress column dendrogram
You can also suppress the cbar as indicated by Yacine.
Actually the easiest way to do that would be by using the tree_kwd argument to set the linewidts parameter of the underlying matplotlib.collections.LineCollection object to zero.
clustermap(YOUR_DATA, tree_kws={"linewidths": 0.})