clonalOverlay {scRepertoire}R Documentation

Visualize distribution of clonal frequency overlaid on dimensional reduction plots

Description

This function allows the user to visualize the clonal expansion by overlaying the cells with specific clonal frequency onto the dimensional reduction plots in Seurat. Credit to the idea goes to Dr. Carmona and his work with [ProjectTIL](https://github.com/carmonalab/ProjecTILs).

Usage

clonalOverlay(
  sc,
  reduction = NULL,
  freq.cutpoint = 30,
  bins = 25,
  facet = NULL
)

Arguments

sc

The seurat or SCE object to visualize after combineExpression().

reduction

The dimensional reduction to visualize

freq.cutpoint

The overlay cutpoint to include, this corresponds to the Frequency variable in the single-cell objecter

bins

The number of contours to the overlay

facet

meta data variable to facet the comparison

Value

ggplot object

Author(s)

Francesco Mazziotta, Nick Borcherding

Examples

#Getting the combined contigs
combined <- combineTCR(contig_list, rep(c("PX", "PY", "PZ"), each=2), 
rep(c("P", "T"), 3), cells ="T-AB")

#Getting a sample of a Seurat object
screp_example <- get(data("screp_example"))
sce <- suppressMessages(Seurat::UpdateSeuratObject(screp_example))

#Using combineExpresion()
sce <- combineExpression(combined, sce)

#Using clonalOverlay()
clonalOverlay(sce, freq.cutpoint = 0.3, bins = 5) 


[Package scRepertoire version 1.4.0 Index]