plotConditionsProfiles: Plot feature profile along distance for multiple conditions

In iaaka/visutils: QC, analyse and visualize visium

Plot feature profile along distance for multiple conditions

Description

Plot feature profile along distance for multiple conditions

Usage

plotConditionsProfiles(
  m,
  feature,
  conditions,
  cols = NULL,
  ltys = 1,
  sd.mult = 2,
  legend. = TRUE,
  ylim = NULL,
  xlim = NULL,
  scaleY = FALSE,
  area.opacity = 0.2,
  lwd = 2,
  xlab = "Distance (spots)",
  ylab = "Abundance",
  main = "",
  cilim = c(-Inf, Inf)
)

Arguments

m	3d (distance/feature/sample) numeric matrix with summarized data (output of makeDistFeatureSampleTable)
feature	single character, name of feature to be plotted (from second dimension of m)
conditions	vector specifying conditions of all samples (along third dimension of m)
cols	named (by conditions) color vector. Only conditions mentioned here will be shown. Colours are aoutogenerated by char2col if null (default)
sd.mult	width of CI shown by shade expressed in standart deviations of mean
legend.	logical, whether logend should be plotted, or list with parameters to be passed to legend function.
ylim	ylim to be set, set by data if NULL (default)
scaleY	whether all features should be scaled by its max value (to bring all features to the same scale)
area.opacity	opacity of CI shade
lwd	line width
xlab, ylab, main	plot annotation
cilim	numerical vector with two values, gives lower and apper values to truncate CI. NULL (to truncation) by default.
...	other parameters to be passed to plot

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