supercell_GeneGenePlot: Gene-gene correlation plot

In SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells

Gene-gene correlation plot

Description

Plots gene-gene expression and computes their correaltion

Usage

supercell_GeneGenePlot(
  ge,
  gene_x,
  gene_y,
  supercell_size = NULL,
  clusters = NULL,
  color.use = NULL,
  idents = NULL,
  pt.size = 1,
  alpha = 0.9,
  x.max = NULL,
  y.max = NULL,
  same.x.lims = FALSE,
  same.y.lims = FALSE,
  ncol = NULL,
  combine = TRUE,
  sort.by.corr = TRUE
)

Arguments

ge	a gene expression matrix of super-cells (ncol same as number of super-cells)
gene_x	gene or vector of genes (if vector, has to be the same lenght as gene_y)
gene_y	gene or vector of genes (if vector, has to be the same lenght as gene_x)
supercell_size	a vector with supercell size (ordered the same way as in ge)
clusters	a vector with clustering information (ordered the same way as in ge)
color.use	colors for idents
idents	idents (clusters) to plot (default all)
pt.size	point size (if supercells have identical sizes)
alpha	transparency
x.max	max of x axis
y.max	max of y axis
same.x.lims	same x axis for all plots
same.y.lims	same y axis for all plots
ncol	number of colums in combined plot
combine	combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot
sort.by.corr	whether to sort plots by absolute value of correlation (fist plot genes with largest (anti-)correlation)

Value

a list with components

• p - is a combined ggplot or list of ggplots if combine = TRUE

• w.cor - weighted correlation between genes

a list, where

SuperCell documentation built on Oct. 25, 2024, 5:07 p.m.