flowplot: Draw expression dotplots

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

Draw expression dotplots

Description

It draws the classical flow cytometry dotplot faceting two markers. Multiple dot plots can be plotted if x.axis and y.axis are specified with multiple markers.

Usage

flowplot(
  fcs.SCE,
  assay.i = "normalized",
  x.axis,
  y.axis,
  densities = T,
  color.by,
  select.values.color = "all",
  size = 0.5,
  colors = NULL
)

Arguments

fcs.SCE	A fcs.SCE object generated through FlowCT::fcs.SCE(). By default, the matrix used is the arcsinh transformed.
assay.i	Name of matrix stored in the fcs.SCE object from which calculate correlation. Default = "normalized".
x.axis	Vector of markers to draw x-axis on the dotplots. Length must be the same of y.axis because each marker has its parter in y.axis.
y.axis	Vector of markers to draw y-axis on the dotplots. Length must be the same of x.axis because each marker has its parter in x.axis.
densities	Logical indicating if densities must be drawn in each plot. Default = TRUE.
color.by	Variable from (from colData(fcs.SCE)) for events coloring.
select.values.color	Vector of values taken from color.by option to include in the coloring. Default = "all".
size	Point (event) size. Default = 0.5.
colors	Vector with colors for plotting. Default = NULL (i.e., it will choose automatically a vector of colors according to FlowCT::div.colors()).

Examples

## Not run: 
flowplot(fcs, x.axis = c("FSC_A", "CD4", "CD62L"), y.axis = c("SSC_A", "CD8", "CD45"),
    color.by = "SOM", select.values.color = 1:10)

## End(Not run)

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