How to order the legend

[WeipengMO]

Hi @DingWB ,

Thank you for developing such an excellent tool! I am currently working with PyComplexHeatmap and encountered a specific need regarding the order of the legend.

In the example provided here, I would like to modify the order of the legend so that it displays "AB" followed by "CD."

Could you kindly guide me on how to customize the legend's order in this scenario?

Below is an image to illustrate what I mean:

Thank you in advance for your help!

Best,
Weipeng

[DingWB]

Hi @WeipengMO ,

This is an interesting problem, I have never thought about it.
The order of legends is determined by the variable legend_list, I would suggest you change the order of self.legend_list and plot. For example:
For annotations only:

plt.figure(figsize=(4, 8))
col_ha = HeatmapAnnotation(
            **, plot=False
)
# change the order of legend_list
col_ha.legend_list=[col_ha.legend_list[i] for i in [the target order]]
col_ha.plot_annotations()
plt.show()

Similarly, for ClusterMapPlotter:

plt.figure(figsize=(4, 8))
cm = ClusterMapPlotter(
            **, plot=False
)
# change the order of legend_list
cm.legend_list=[cm.legend_list[i] for i in [the target order]]
cm.plot()
# if plot_legend:
# if legend_anchor == "auto":
if (
not cm.right_annotation is None
and cm.legend_side == "right"
):
    legend_anchor = "ax"
else:
    legend_anchor = "ax_heatmap"
if legend_anchor == "ax_heatmap":
	cm.plot_legends(ax=cm.ax_heatmap)
else:
	cm.plot_legends(ax=cm.ax)

cm.post_processing()
plt.show()

[WeipengMO]

Thank you for your kind reply! I'll give it a try. 🫡

[WeipengMO]

Hi @DingWB,

I noticed that in the Class, the legends are automatically sorted by title, which causes the output plots not to follow the input order of the legend titles. I suggest adding a sort_legend parameter to allow users to control whether the legends should be sorted or not.

PyComplexHeatmap/PyComplexHeatmap/dotHeatmap.py

Line 648 in 09065ff

if len(self.legend_list) > 1:

PyComplexHeatmap/PyComplexHeatmap/annotations.py

Line 1821 in 09065ff

if len(self.legend_list) > 1:

PyComplexHeatmap/PyComplexHeatmap/clustermap.py

Line 2251 in 09065ff

if len(self.legend_list) > 1:

PyComplexHeatmap/PyComplexHeatmap/oncoPrint.py

Line 519 in 09065ff

if len(self.legend_list) > 1:

For example, the following code can be adjusted. By adding sort_legend, users can decide whether to keep the original order or sort the legends based on title.

if len(self.legend_list) > 1 and self.sort_legend:
    self.legend_list = sorted(self.legend_list, key=lambda x: x[3])

[DingWB]

No, the legends are not sorted by title. They are sorted by length. The idea is to plot the longest legend first, then the short one.
Otherwise, if you plot the short one first, there will be no space for the longer legend.

[DingWB]

Hi @WeipengMO ,

As you requested, I just added a parameter legend_order to both HeatmapAnnotation and ClusterMapPlotter.

legend_order: str, bool or list
control the order of legends, default is 'auto', sorted by length of legend.
could also be True/False or a list (or tuple). if a list / tuple is provided,
values should be the label (title) of each legend.

See example:

Could you please install the latest version from Github (pip uninstall -y PyComplexHeatmap && pip install git+https://github.com/DingWB/PyComplexHeatmap ), try and test whether it works or not?

[WeipengMO]

Hi @DingWB ,

Thank you for your prompt response and for adding the legend_order parameter to both HeatmapAnnotation and ClusterMapPlotter. I've installed the latest version from GitHub and tested it. The update works out perfectly!

In addition, I noticed that the dotHeatmap.py and oncoPrint.py modules do not yet have the legend_order parameter implemented. Would it be beneficial to include this parameter in these modules as well?

Thanks again for your help!

Best,
Weipeng

[DingWB]

I appreciate your reminder. Just implemented it in dotHeatmap.py and oncoPrint.py. Could you please reinstall it again and test it?

The parameter is the same, cause oncoPrintPlotter and DotClustermapPlotter are inherited from ClusterMapPlotter.

[WeipengMO]

@DingWB , I have tested it. This works out! 👍👍👍