stereo.plots.PlotTimeSeries.paga_time_series_plot#

PlotTimeSeries.paga_time_series_plot(use_col, batch_col, groups=None, height=10, width=0, palette='tab20', link_alpha=0.5, spot_size=1, dpt_col='dpt_pseudotime')[source]#

spatial trajectory plot for paga in time_series multiple slice dataset

Parameters:

  • use_col (str) – the col in obs representing celltype or clustering.

  • batch_col (str) – the col in obs representing different slice of time series.

  • groups (Optional[str]) – the particular celltype that will show, default None means show all the celltype in use_col.

  • height (Optional[float]) – height of figure.

  • width (Optional[float]) – width of figure.

  • palette (Optional[str]) – color palette to paint different celltypes.

  • link_alpha (Optional[float]) – alpha of the bezierpath, from 0 to 1.

  • spot_size (Optional[int]) – the size of each cell scatter.

  • dpt_col (Optional[str]) – the col in obs representing dpt pseudotime.

  • reorganize_coordinate –

    if the data is merged from several slices, whether to reorganize the coordinates of the obs(cells), if set it to a number, like 2, the coordinates will be reorganized to 2 columns on coordinate system as below:

    data1 data2
    data3 data4
    data5 …
    … …

    if set it to False, the coordinates will not be changed.

  • horizontal_offset_additional – the additional offset between each slice on horizontal direction while reorganizing coordinates.

  • vertical_offset_additional – the additional offset between each slice on vertical direction while reorganizing coordinates.

Returns:

a fig object