plot_stat: Plot aggregated data from a GatingSet

In VoisinneG/flowR: R-shiny interface for the analysis of flow cytometry data

Description

Plot aggregated data from a GatingSet

Usage

plot_stat(
  df = NULL,
  gs,
  sample = NULL,
  subset = NULL,
  spill = NULL,
  metadata = NULL,
  transformation = NULL,
  stat_function = "mean",
  y_trans = identity_trans(),
  apply_inverse = TRUE,
  yvar = NULL,
  var_names = NULL,
  scale = FALSE,
  plot_type = "heatmap",
  plot_args = list(),
  options = list()
)

Arguments

df	a data.frame with plot data resulting from a call of get_plot_data. Supersedes parameters 'gs', 'sample', 'spill'
gs	a GatingSet
sample	Names of samples from the GatingSet (as returned by pData(gs)$name)
subset	Names of subsets from the GatingSet (as returned by gs_get_pop_paths(gs))
spill	spillover matrix. If NULL, uncompensated data is used for gating and plotting.
metadata	a data.frame containing metadata associated to samples. Must have a column name used for mapping.
transformation	A list of trans objects. Each element must be named after a parameter and contain the transfomation to apply for this parameter. If NULL, the default transformation 'y_trans' is applied.
stat_function	Name of the function to be applied on transformed data for each sample and subset.
y_trans	Default trans object (set to 'identity_trans()' by default). Used only if parameter 'transformation' is NULL.
apply_inverse	logical; Apply inverse transformation before returning the data.
yvar	Names of the variables for which to compute statistics
var_names	Replace 'yvar' with custom names
scale	logical; Should data be scaled for each 'yvar' variable?
plot_type	name of the plot type
plot_args	list of plot parameters passed to the plot function. Plot parameters depend on the plot type selected.
options	list of plot format options passed to format_plot()

Value

a list with a plot and the corresponding plot data

VoisinneG/flowR documentation built on June 1, 2021, 6:42 p.m.