CreateGraphReport: Graph Report Generation

In IFC: Tools for Imaging Flow Cytometry

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.

Value

a list with onepage, layout, layout_matrix, graphs, grobs, and stats.

IFC documentation built on Sept. 14, 2023, 1:08 a.m.