flowsom.pl.plot_2D_scatters

flowsom.pl.plot_2D_scatters#

flowsom.pl.plot_2D_scatters(fsom, channelpairs, clusters=None, metaclusters=None, max_background_points=3000, size_background_points=0.5, max_points=1000, size_points=0.5, x_lim=None, y_lim=None, xy_labels=None, density=True, centers=True, colors=None, plot_file='2DScatterPlots.png', title=None)#

Function to draw 2D scatter plots of FlowSOM (meta)clusters.

Parameters:

  • fsom (FlowSOM) – A FlowSOM object

  • channelpairs (list) – A list of list with channels/markers to plot

  • clusters (list) – A list of lists with cluster ids to plot

  • metaclusters (list) – A list of lists with metacluster ids to plot

  • max_background_points (int) – Maximum number of background points to plot. Default is 3000.

  • size_background_points (float) – Size of background points. Default is 0.5.

  • max_points (int) – Maximum number of points to plot. Default is 1000.

  • size_points (float) – Size of points. Default is 0.5.

  • x_lim (tuple) – Limits for the x-axis. Default is None.

  • y_lim (tuple) – Limits for the y-axis. Default is None.

  • xy_labels (list) – Labels for the x and y axis. Default is [“marker”]. Can be ‘marker’ and/or ‘channel’.

  • density (boolean) – Whether to plot density or not. Default is True.

  • centers (boolean) – Whether to plot centers or not. Default is True.

  • colors (np.array | None (default: None))

  • plot_file (str (default: '2DScatterPlots.png'))

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