Batch creates graphical an statistical report.
BatchReport(
fileName,
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",
display_progress = TRUE,
...
)path to file(s).
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 single 'fileName'. NA value will result in an empty place.
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 of first element of 'fileName' -%p: with first parent directory of first element of 'fileName' -%e: with extension of first element of 'fileName' (without leading .) -%s: with shortname from first element of 'fileName' (i.e. basename without extension). Exported file(s) extension(s) will be deduced from this pattern. Note that has to be a .pdf and/or .csv.
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.
an `IFC_gating` object as extracted by readGatingStrategy(). Default is missing. If not missing, each file provided in 'fileName' will be extracted by readIFC() and 'gating' will be applied by applyGatingStrategy() to the returned object before creating the report
the main title of the document. Default is missing.
whether to add selected graphs for each file by row or not. Deafult is FALSE.
number of files to add before starting a new row or column (depending on 'byrow').
Whether to extract colors from obj in white or black mode. Default is "white".
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.
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.
maximum number of characters to display for labels. Default is 38.
transformation function for density graphs. If missing the default, the BasePop[[1]]$densitytrans, if any, will be retrieved, otherwise asinh will be used.
default number of bin used for histogram. Default is missing.
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.
whether to display a progress bar. Default is TRUE.
other parameters to be passed.
It invisibly returns full path of exported .pdf and/or .csv file(s).