mmc.density_plot()
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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 (
str(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 seaborne.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
- adata (