Coexpression of selected genes — GEX_coexpression

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.

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)
#> Calculating coexpression for 2 genes with 21 cells
#>   col.1 col.2 gene.1 gene.2 coex.coef perc.single.positive
#> 1     1     2   CD19   CD83  41.93548             41.93548