mmc.density_plot()

mmochi.landmarking.density_plot(adata, marker, batch, batch_key=utils.BATCH_KEY, data_key=utils.DATA_KEY, bw_adjust=0, step=0.1, exclude_zeroes=True)

Creates density plot of a single batch for a single marker for a given data_key. Marks location of landmark(s) with small black line(s) on x axis.

Parameters:

• adata (AnnData) – AnnData to use with a batch in batch_key in .obs, and data in .obsm[data_key].

• marker (str) – Marker to be plotted. Uses mmc.utils.get_data to find the marker.

• batch_key (str (default: utils.BATCH_KEY)) – Category in .obs where batch is.

• batch (str) – Label in .obs[batch_key] to be plotted.

• data_key (Union[str, list] (default: utils.DATA_KEY)) – Label in .obsm to be plotted.

• bw_adjust (float (default: 0)) – Scalar to multiply bandwidth smoothing method used by seaborn.kdeplot. See seaborn.kdeplot for more details. Use 0 to plot a histogram.

• step (float (default: 0.1)) – Size of x ticks on histogram.

• exclude_zeroes (bool (default: True)) – If True, only displays non-zero events, which can be useful for visualization of data with many events with zero protein expression