supercell_GeneGenePlot: 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
)

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

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)