plot_similarity: Plot repertoire overlap

In friedue/SCEdjvdj: Single-cell VDJ Tools for SCE objects

Description

Plot repertoire overlap

Usage

plot_similarity(
  SCE_in,
  clonotype_col = "cdr3_nt",
  cluster_col,
  method = abdiv::jaccard,
  plot_colors = NULL,
  ...
)

Arguments

clonotype_col	meta.data column containing clonotype IDs to use for calculating overlap
cluster_col	meta.data column containing cluster IDs to use for calculating overlap. Any grouping column from colData(SCE_in) will do.
method	Method to use for calculating similarity between clusters
plot_colors	Character vector containing colors for plotting
...	Additional arguments to pass to ggplot
sce_in	SCE object containing V(D)J data or matrix containing similarity values to plot

Value

ggplot object

Author(s)

djvdj authors

friedue/SCEdjvdj documentation built on April 21, 2021, 7:54 a.m.