flowsom.pl.plot_marker

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flowsom.pl.plot_marker#

flowsom.pl.plot_marker(fsom, marker, ref_markers=None, lim=None, cmap=<matplotlib.colors.LinearSegmentedColormap object>, **kwargs)#

Plot FlowSOM grid or tree, colored by node values for a specific marker.

Parameters:

  • fsom (FlowSOM) – A FlowSOM object

  • marker (str, int) – A marker to plot. Can be a channel/marker/index.

  • ref_markers (np.array, list) – Is used to determine relative scale of the marker that will be plotted. Default are all markers used in the clustering.

  • lim (tuple) – Limits for the color scale

  • cmap (default: <matplotlib.colors.LinearSegmentedColormap object at 0x7a0adaf1c400>) – A colormap to use

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