VizVDJDist: Visualize clonotype distributions

In j-andrews7/EZscRNA: Simple Convenience Functions for High-Level scRNA-Seq Analysis

Description

VizVDJDist visualizes clonotype distributions for each sample in a seurat object as histograms as well as barcharts comparing clonotype proportions between them.

Usage

VizVDJDist(scrna, outdir, g.by = NULL, o.by = NULL, n.clono.c = 10,
  n.clono.g = NULL)

Arguments

scrna	Seurat object with clonotype data added to metadata with AddClonotype.
outdir	Path to output directory.
g.by	Metadata column to group samples by. If not provided, only histograms of clonotypes will be saved.
o.by	Vector containing names of members of each group to sort by within the group. Ignored if g.by is NULL. Should contain one instance of each potential value in g.by column if provided.
n.clono.c	Number of top clonotypes to plot for comparison barchart. Ignored if g.by is NULL.
n.clono.g	Number of clonotypes to show in group-specific histograms. All are shown by default.

Details

Cells with no clonotypes are still included in determining clonotype frequencies, but NA is removed from subsequent graphs.

Author(s)

Jared Andrews

j-andrews7/EZscRNA documentation built on Feb. 24, 2020, 10:37 a.m.