plotVisiumMultyColours: Plot multiple numerical values (gene expression or cell...

In iaaka/visutils: QC, analyse and visualize visium

Plot multiple numerical values (gene expression or cell abundances) on H&E image

Description

Each spot is colored by weighted mean colour. Opacity of spot is proportional to maximal feature intensity.

Usage

plotVisiumMultyColours(
  v,
  z,
  cols = NULL,
  zfun = function(x) x^2,
  scale.per.colour = TRUE,
  min.opacity = 0,
  title.adj = c(0, -0.5),
  legend.ncol = 1,
  ...
)

Arguments

v	Seurat object
z	matrix with values (in columns) to be plotted
cols	colors to be used for columns in z
zfun	function to transform values in z (z^2 is default)
scale.per.colour	logical, specifies whether each color should cover whole range (that is, should z be scaled per column)
min.opacity	int from 0 to 255. Minimal spot opacity. Default is 0, that means that spots with low intensity of all features will be almost transparent. Set it higer if you want at least one feature to be visible in each spot.
title.adj	legend title adj (to be passed to text function)
legend.ncol	number of legend columns. Set to 0 to suppress legend plotting.
...	other parameters to be passed to plotVisium

Value

data.frame with user spot coordinates

iaaka/visutils documentation built on Jan. 17, 2025, 11:29 p.m.