plot_embed_clonotype: plot_embed_clonotype

In garber-lab/VDJChef: VDJChef for vdj analysis

plot_embed_clonotype

Description

Visual and highlight clonotypes given an embedding

Usage

plot_embed_clonotype(
  input,
  title = "",
  clonotype_id,
  clonotype_by,
  color_by,
  facet_by = NULL,
  ncol = NULL,
  label = FALSE,
  size = 1.5,
  alpha = 0.3,
  colors = NULL,
  theme = "classic",
  legend_dot_size = 1.5,
  xcol = "x",
  ycol = "y",
  reduction = "umap",
  text_sizes = c(20, 10, 5, 10),
  shuffle = F
)

Arguments

input	ExpressionSet or Seurat Object
title	Title of the ggplot2 plot
clonotype_id	Clonotype ID among values listed by "clonotype_by" parameter
clonotype_by	the label of the column in metadata that defines clonotypes
color_by	What to color points by, either "UMI_sum", or pData categorial variable, ignored if gene is provided
facet_by	What to break the plots by
ncol	How many columns if faceting
label	if true, labels of "color_by" will be visualized on embedding
size	The size of the points
alpha	The transparency of the points
colors	What colors to utilize for categorial data. Be sure it is of the proper length!
theme	display theme
legend_dot_size	Size of dot in legend
xcol	pData column to use for x axis
ycol	pData column to use for y axis
reduction	the reduction key for Seurat objects
text_sizes	text sizes for multiple components of the ggplot figure
shuffle	change order of labels

Examples

# library
library(Seurat)

# analyzed data with tcr
data("seu_analyzed")

# get clonotype highlighted on embedding
plot_embed_clonotype(seu_analyzed, clonotype_by = "cdr3s_aa", clonotype_id = "TRB:CASNPSTGGGGEQYF;TRA:CAVMDSNYQLIW",
                     color_by = "seurat_clusters")
plot_embed_clonotype(seu_analyzed, clonotype_by = "cdr3s_aa", clonotype_id = "TRB:CASNPSTGGGGEQYF;TRA:CAVMDSNYQLIW",
                     color_by = "seurat_clusters", reduction = "tsne", label = T)

garber-lab/VDJChef documentation built on Aug. 30, 2022, 3:30 a.m.