gradient heatmap

[hjack123]

Is there a way to plot gradient heatmap for the clinical annotation

[pjb7687]

Please leave an example here, and I will try to add it.

[hjack123]

df_stagecode = df_all_annotations[df_all_annotations.index == 'American Joint Committee on Cancer Tumor Stage Code']
uniq_annots = sorted(pd.unique(df_stagecode.values.ravel()))
annotations['American Joint Committee on Cancer Tumor Stage Code'] = {
'annotations': df_stagecode,
'colors': {k: v for k, v in zip(uniq_annots, cmap(np.linspace(0, 1, len(uniq_annots), dtype=float)))},
'order': 2
}

take your code for example: df_stagecode.values will be np.array([1,1.1,1.2,1.3,nan]) and uses 'Reds' or 'Greys' as color, and leave nan as white or grey. This could be dosages used for patients and annotated on the top of the oncoprint for each pt