plotFeatureProfiles: Plots features profiles

In iaaka/visutils: QC, analyse and visualize visium

Plots features profiles

Description

along distance. Shows mean abundance as line and CI as shade.

Usage

plotFeatureProfiles(
  m,
  features,
  cols = NULL,
  sd.mult = 2,
  legend. = TRUE,
  ylim = NULL,
  scaleY = TRUE,
  area.opacity = 0.2,
  lwd = 2,
  xlab = "Distance (spots)",
  ylab = "Relative abundance",
  main = "",
  xlim = NULL,
  cilim = c(-Inf, Inf),
  ...
)

Arguments

m	3d (distance/feature/sample) numeric matrix with summarized data (output of makeDistFeatureSampleTable)
features	features (indexes along third dimension of m)
cols	names (by feature names) colour vector
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.