plot_heatmap_clonotypes: plot_heatmap_clonotypes

In garber-lab/VDJChef: VDJChef for vdj analysis

plot_heatmap_clonotypes

Description

Visualize clonal expansion by heatmap. Default shows the clonal expansion of the top 20 unique clonotypes across all of a grouping variable, or the number of clones of the top 20 clonotypes per each facet by multiple grouping variables Bottom row annotation shows the total number of clones in each grouping variable

Usage

plot_heatmap_clonotypes(
  input,
  clonotype_by,
  patient_by = NULL,
  sample_by = NULL,
  group_by = NULL,
  sort_by = NULL,
  sort_id = NULL,
  ntop = 20,
  Count_limit = NULL
)

Arguments

input	Seurat Object or ExpressionSet
clonotype_by	meta.data or pData column name for clonotype ID's
patient_by	meta.data or pData column name for patient
sample_by	meta.data or pData column name for sample
group_by	What to color points by, either "UMI_sum", or meta.data or pData column name, ignored if gene is provided
sort_by	The metadata column for sorting
sort_id	The value in the metadata column for sorting
ntop	the number of top clonotypes to return
Count_limit	count limit for plot legend

Examples

# library
library(Seurat)

# analyzed data with tcr
data("seu_analyzed")

# get clonotype highlighted on embedding
plot_heatmap_clonotypes(seu_analyzed, clonotype_by = "cdr3s_aa", group_by = "seurat_clusters")
plot_heatmap_clonotypes(seu_analyzed, clonotype_by = "cdr3s_aa", group_by = "seurat_clusters", ntop = 10)

# some additional uses
plot_heatmap_clonotypes(pfizer, clonotype_by = "CTaa", patient_by = "Patient", sample_by = "Sample") # ClonotypeIDs not listed, as not directly comparable across different patients
plot_heatmap_clonotypes(pfizer, clonotype_by = "CTaa", group_by = "Sample_Type")

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