pycallingcards.plotting.dotplot_sc_mu#

pycallingcards.plotting.dotplot_sc_mu(mdata, adata_cc='CC', adata='RNA', result='pair', cluster_name='RNA:cluster', rate=50, figsize=(10, 120), size=1, cmap1='Reds', cmap2='BuPu', title='DE binding & RNA', topspace=0.977, legend=False, cax1=[-0.05, -0.2, 0.03, 0.25], cax2=[0.0, -0.2, 0.03, 0.25], save=False)[source]#

Designed for mudata object. Plot ranking of peaks.

Parameters:

  • mdata (MuData) – mdata for both CC and RNA.

  • adata_cc (str (default: 'CC')) – Name for CC data. Anndata is mdata[adata_cc].

  • adata (str (default: 'RNA')) – Name for RNA data. Anndata is mdata[adata].

  • result (str (default: 'pair')) – pd.DataFrame of result gain from cc.tl.pair_peak_gene_sc with ‘Peak’ and ‘Gene’ columns.

  • cluster_name (str (default: 'RNA:cluster')) – The name of cluster in adata_cc and adata.

  • rate (float (default: 50)) – Rate to control the dot size.

  • figsize (Tuple[int, int] (default: (10, 120))) – The size of the figure.

  • size (int (default: 1)) – The size of relative size of text.

  • cmap – The colormap of the plot for bindings.

  • cmap – The colormap of the plot for genes.

  • title (str (default: 'DE binding & RNA')) – The title of the plot.

  • topspace (float (default: 0.977)) – Parameter to control the title position.

  • legend (bool (default: False)) – If True, it would show the legend.

  • cax1 (list (default: [-0.05, -0.2, 0.03, 0.25])) – The position of the legend for genes.

  • cax2 (list (default: [0.0, -0.2, 0.03, 0.25])) – The position of the legend for bindings.

  • save (bool (default: False)) – Could be bool or str indicating the file name it would be saved as. If True, a default name will be given and the plot would be saved as a png file.

Example:

>>> import pycallingcards as cc
>>> mdata = cc.datasets.mousecortex_data(data="Mudata")
>>> cc.pl.dotplot_sc_mu(mdata)