BatchReport {IFC}

Batch Generation of Graphical and Statistic Report

Description

Batch creates graphical an statistical report.

Usage

BatchReport(
  fileName,
  obj,
  selection,
  write_to,
  overwrite = FALSE,
  gating,
  main,
  byrow = FALSE,
  times = 5,
  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

fileName, obj

either one or the other. Path to file(s) to read from for 'fileName' or list of 'IFC_data' objects for obj.

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 for each 'fileName' or ”obj'.
NA value will result in an empty place. When missing, it will be determined by the whole layout of 1st 'fileName' or 'obj' with 'gating' applied when provided

write_to

pattern used to export file(s). Placeholders, like c("%d/%s_fromR.pdf", "%d/%s_fromR.csv"), will be substituted:
-%d: with full path directory
-%p: with first parent directory
-%e: with extension (without leading .)
-%s: with shortname (i.e. basename without extension).
Exported file(s) extension(s) will be deduced from this pattern using either 1st 'fileName' or 'obj'. Note that has to be a .pdf and/or .csv.

overwrite

whether to overwrite file or not. Default is FALSE. Note that if TRUE, it will overwrite file. In addition a warning message will be sent.

gating

an 'IFC_gating' object as extracted by readGatingStrategy(). Default is missing. If not missing, each ‘IFC_data' provided in ’obj' or read from 'fileName' will be passed to applyGatingStrategy() before creating the report.

main

the main title of the document. Default is missing.

byrow

whether to add selected graphs for each file by row or not. Default is FALSE.

times

number of files to add before starting a new row or column (depending on 'byrow').

color_mode

Whether to extract colors 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

It invisibly returns full path of exported .pdf and/or .csv file(s).