calour
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biocore
Robust quantiles
Would be nice if the heatmap colors were scaled to robust quantiles rather than the extreme values
See seaborn robust parameter http://seaborn.pydata.org/generated/seaborn.heatmap.html
Its honestly the only reason why I use seaborn anymore. Is there any interest in adding this into calour?
looks like in seaborn what they do is: if vmin is None: vmin = np.percentile(calc_data, 2) if robust else calc_data.min() if vmax is None: vmax = np.percentile(calc_data, 98) if robust else calc_data.max()
so should be a piece of tasty cake :) (main question is how to integrate into the calour heatmap api - what parameter...)
seaborn is just doing robust=True for their parameter I think this should be an easy first pass.
Matplotlib also has vmin/vmax parameters, where you can specify the specific quantiles.
P.S. Is midpoint normalize implemented in calour? https://matplotlib.org/users/colormapnorms.html Seaborn seems to have multiple bugs popping up recently and now it can't perform midpoint normalize anymore -- may issue a bug report in the near future.
On Tue, Jun 25, 2019 at 8:59 AM amnona [email protected] wrote:
looks like in seaborn what they do is: if vmin is None: vmin = np.percentile(calc_data, 2) if robust else calc_data.min() if vmax is None: vmax = np.percentile(calc_data, 98) if robust else calc_data.max()
so should be a piece of tasty cake :) (main question is how to integrate into the calour heatmap api - what parameter...)
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