GEX_coexpression_coefficient: Coexpression of selected genes

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Coexpression of selected genes

Description

Returns eiter a plot or numeric data of coexpression levels of selected genes.Coexpression % is calculated as the quotient of double positive cells (counts \> 0) and the sum of total cells positive for either genes.

Usage

GEX_coexpression_coefficient(GEX, genes, subsample.n, plot.dotmap)

Arguments

GEX	GEX seurat object generated with VDJ_GEX_matrix (VDJ_GEX_matrix.output\[\[2\]\])
genes	Character vector. At least 2 genes present in rownames(GEX). Use "all" to include all genes. The number of comparisons to make is the length(genes)! (factorial). More than 100 genes are not recommended.
subsample.n	Interger. Number of cells to subsample. If set to 100, 100 cells will be randomly sampled for the calculation
plot.dotmap	Boolean. Whether to return a plot

Value

Returns a dataframe if pot.dotmap == F or a ggplot if plot.dotmap == T detailing the coexpression levels of selected genes within the given cell population

Examples

#To return a dataframe with coefficients
#GEX_coexpression_coefficient(GEX = VDJ_GEX_matrix.output[[2]]
#, genes = c("CD19", "EBF1","SDC1"), subsample.n = "none", plot.dotmap = FALSE)

#To return a dotplot detailing coexpression and overall expression
GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]]
, genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.