multidensity: Density plots with expression values overlapped

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

Density plots with expression values overlapped

Description

This function draws multidensity plot with all FCS files included in a fcs.SCE object. If there are more files than limit specified in ridgeline.lim, instead of plottting density in a ridge-way all density lines will be overlapped.

Usage

multidensity(
  fcs.SCE,
  assay.i,
  show.markers = "all",
  color.by = NULL,
  subsampling = NULL,
  interactive = F,
  ridgeline.lim = 15,
  colors = NULL
)

Arguments

fcs.SCE	A fcs.SCE object generated through FlowCT::fcs.SCE().
assay.i	Name of matrix stored in the fcs.SCE object from which calculate correlation. Default = "normalized".
show.markers	Vector with markers to plot. Default = "all".
color.by	Variable name (from colData(fcs.SCE)) for lines coloring.
subsampling	Numeric value indicating how many events use to calculate density lines and speed up plotting. Default = NULL.
interactive	Logical indicating if the user can interact with the (only overlapping-lines) plot. Default = FALSE.
ridgeline.lim	Numeric value specifying the limit for shifting from ridgeline-mode to overlapping-lines plot. Default = 15.
colors	Vector with colors for plotting (only available for no-ridgeline plot). Default = NULL (i.e., it will choose automatically a vector of colors according to FlowCT::div.colors()).

Examples

## Not run: 
multidensity(fcs.SCE = fcs, assay.i = "normalized", subsampling = 1000)
multidensity(fcs, assay.i = 2, color.by = "file_name", ridgeline.lim = 0, 
     show.markers = c("CD62L", "CD4"), interactive = T)

## End(Not run)

jgarces02/FlowCT documentation built on March 28, 2023, 12:42 p.m.