CreateGraphReport: Graph Report Generation
In gitdemont/IFC: Tools for Imaging Flow Cytometry

CreateGraphReport

R Documentation

Graph Report Generation

Description

Generates graph report (plot + statistics) from 'IFC_data' object.

Usage

CreateGraphReport(
  obj,
  selection,
  onepage = TRUE,
  color_mode = c("white", "black")[1],
  add_key = "panel",
  precision = c("light", "full")[1],
  trunc_labels = 38,
  trans = "asinh",
  bin,
  viewport = "ideas",
  backend = "lattice",
  display_progress = TRUE,
  ...
)

Arguments

`obj`	an 'IFC_data' object extracted with features extracted.
`selection`	indices of desired graphs. It can be provided as an integer vector or as a matrix. In such case, the layout of the matrix will reflect the layout of the extracted graphs. NA value will result in an empty place. Otherwise, when 'selection' is provided as a vector not identical to seq_along(obj$graphs), 'onepage' parameter will be set to FALSE. Note that indices are read from left to right, from top to bottom. Default is missing for extracting all graphs.
`onepage`	whether to generate a pdf with all graphs on one page or not. Default is TRUE.
`color_mode`	Whether to extract colors from obj in white or black mode. Default is "white".
`add_key`	whether to draw a "global" key under title or in the first "panel" or "both". Default is "panel". Accepted values are either: FALSE, "panel", "global", "both" or c("panel", "global"). Note that it only applies when display is seen as overlaying populations.
`precision`	when graphs is a 2D scatter with population overlay, this argument controls amount of information displayed. Default is "light". -"light", the default, will only display points of same coordinates that are among the other layers. -"full" will display all the layers.
`trunc_labels`	maximum number of characters to display for labels. Default is 38.
`trans`	name of the transformation function for density graphs. If missing the default, the BasePop[[1]]$densitytrans, if any, will be retrieved, otherwise "asinh" will be used.
`bin`	default number of bin used for histogram. 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.
`display_progress`	whether to display a progress bar. Default is TRUE.
`...`	other parameters to be passed.