Extract fluorescence distribution along a specified channel from the gating set as defined in the gating strategy file and re-calculate data to events per volume.
Usage
makefdmat(
gs,
name.dict = ".",
foN.dict = ".",
type.dict = ".",
expo = TRUE,
expo.gate = ".",
expo.name = ".",
expo.type = ".",
expo.folder = ".",
rcv = ".",
verbose = ".",
dev = FALSE
)Arguments
- gs
A gating set as produced by
makeAddGatingSet.- name.dict
Character length one. The name of the dictionary. If left at the default '.', the value as defined in the settings file (key 'dD_dict_name') will be used.
- foN.dict
Character length one. The name of the folder where the dictionary resides. If left at the default '.', the value as defined in the settings file (key 'foN_dictionary') will be used.
- type.dict
Character length one. The filetype of the dictionary. Can be one of 'csv' or 'xlsx'. If left at the default '.', the value as defined in the settings file (key 'dD_dict_type') will be used.
- expo
Logical, if extracted data should exported at all.
- expo.gate
Which gate to export. NULL or numeric or character length one. Set to NULL to export data from all those gates defined in the gating strategy where 'keepData' is set to TRUE. Provide a character length one with a gate name or the number of that gate as defined in the gating strategy to export data from this gate only. If left at the default '.', the value as defined in the settings file (key 'dE_exportGate') will be used.
- expo.name
Character length one. The name of the file holding the exported fluorescence distribution(s). If left at the default '.', the value as defined in the settings file (key 'fiN_dataExport') will be used.
- expo.type
Character length one. The filetype of the data export. Possible values are 'csv' and 'xlsx'. If left at the default '.', the value as defined in the settings file (key 'dE_exportType') will be used.
- expo.folder
Character length one. The name of the folder where exported data should reside. If left at the default '.', the value as defined in the settings file (key 'foN_rawData') will be used.
- rcv
Logical. If the fluorescence distributions should be re-calculated to events per volume unit. If left at the default '.', the value as defined in the settings file (key 'dV_doRecalcToVolume') will be used.
- verbose
Logical. If status messages should be displayed. If left at the default '.', the value as defined in the settings file (key 'dV_verbose') will be used.
- dev
Logical. If set to true, a histogram showing the bins and the smoothed mid-points is plotted. (Only intended for development.) Defaults to FALSE.
Value
An object of class-fdmat containing a list holding
an object of class-fdmat_single in each list element, which in
turn contains a matrix holding the fluorescence distribution of a single gate,
and the overall data for events per volume unit in the slot
eventsPerVol.
See also
Other Extraction functions:
addGates(),
makeAddGatingSet(),
makeGatingSet()
Examples
td <- tempdir()
data_source <- "https://github.com/bpollner/data/raw/main/flowdex_examples/flowdex_examples.zip"
check_download_data(td, data_source)
exp_home <- paste0(td, "/flowdex_examples")
old_wd <- getwd()
setwd(exp_home)
#
assign("get_settings_from_flowdex_package_root", TRUE, pos=.GlobalEnv)
# only required to make the examples run automatically
# you should not call 'assign' if you run the examples manually
# the effect of setting 'get_settings_from_flowdex_package_root' to TRUE
# is that the file 'flowdex_settings.R' in 'root' of the installed package
# 'flowdex' will be sourced instead of the one in the user-defined location.
#
gs <- makeAddGatingSet()
#> Reading in fcs files... ok.
#> Producing gating set... Applying fjbiexp transformation... ok.
#> Gating: (1 gate)
#> done!
fdmat <- makefdmat(gs, expo = FALSE) # to NOT export the data
#> DNA+: Extracting binned data on FITC.A (res=220) and recalc. to volume... ok.
fdmat <- makefdmat(gs)
#> DNA+: Extracting binned data on FITC.A (res=220) and recalc. to volume... ok.
#> Exporting data (1 gate) to xlsx...ok.
#
setwd(old_wd)