plotGraph: Plot and Stats Computation for IFC Graph

In gitdemont/IFC: Tools for Imaging Flow Cytometry

Plot and Stats Computation for IFC Graph

Description

Computes plot and stats from a IFC graph

Usage

plotGraph(
  obj,
  graph,
  draw = FALSE,
  stats_print = draw,
  color_mode = c("white", "black")[1],
  add_key = "panel",
  precision = c("light", "full")[1],
  trunc_labels = 38,
  trans = "asinh",
  bin,
  viewport = "ideas",
  backend = "lattice",
  ...
)

Arguments

obj	an 'IFC_data' object extracted with features extracted.
graph	a graph from 'obj' or a list that can be coerced by buildGraph.
draw	whether to draw plot or not. Default is FALSE.
stats_print	whether to print stats or not. Default is given by 'draw' argument.
color_mode	whether to extract colors from 'obj' in white or black mode. Default is "white".
add_key	whether to draw a "global" key under title or in the first "panel" or "both". Default is "panel". Accepted values are either: FALSE, "panel", "global", "both" or c("panel", "global"). Note that it only applies when display is seen as overlaying populations.
precision	when graphs is a 2D scatter with population overlay, this argument controls amount of information displayed. Default is "light". -"light", the default, will only display points of same coordinates that are among the other layers. -"full" will display all the layers.
trunc_labels	maximum number of characters to display for labels. Default is 38.
trans	the name of a transformation function for density graphs. If missing the default, the BasePop[[1]]$densitytrans, if any, will be retrieved, otherwise "asinh" will be used.
bin	number of bin used for histogram / density. Default is missing.
viewport	either "ideas", "data" or "max" defining limits used for the graph. Default is "ideas". -"ideas" will use same limits as the one defined in ideas. -"data" will use data to define limits. -"max" will use data and regions drawn to define limits.
backend	backend used for drawing. Allowed are "lattice", "base", "raster". Default is "lattice". -"lattice" is the original one used in IFC using lattice, -"base" will produce the plot using base, -"raster" uses "base" for plotting but 2D graphs points will be produced as rasterImage. This has the main advantage of being super fast allowing for plotting a huge amount of points while generating smaller objects (in bytes). However, plot quality is impacted with "raster" method and resizing can lead to unpleasant looking.
...	other arguments to be passed.

Value

it invisibly returns a list whose members are:
-stats, a table of statistics computed for the graph, if 'stats_print' was TRUE,
-input, a list with input parameters.

gitdemont/IFC documentation built on Feb. 20, 2025, 12:55 a.m.