Source the settings-list as defined in the settings.R file and
create the object 'stn' in its environment. The settings-file system is
based on functionality from package uniset.
See also
Other Setup functions:
setup_settings()
Examples
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.
#
stn <- fd_update_settings()
str(stn)
#> List of 51
#> $ gen_autoUpdateSettings: logi TRUE
#> $ dV_verbose : logi TRUE
#> $ dV_use_volumeData : logi TRUE
#> $ foN_gating : chr "gating"
#> $ foN_fcsFiles : chr "fcsFiles"
#> $ foN_rawData : chr "rawdata"
#> $ foN_templates : chr "templates"
#> $ foN_dictionary : chr "dictionary"
#> $ foN_plots : chr "plots"
#> $ fiN_gate : chr "polyGate"
#> $ fiN_gateStrat : chr "gateStrat"
#> $ dE_exportType : chr "xlsx"
#> $ dE_exportGate : NULL
#> $ fiN_dataExport : chr "flscData"
#> $ dV_charEventsPerVolume: chr "evpv"
#> $ dV_tx : chr "fjbiexp"
#> $ dV_channel : chr "A$"
#> $ dV_comp : logi FALSE
#> $ dV_gateStratInputType : chr "xlsx"
#> $ dV_dictionaryType : chr "xlsx"
#> $ dV_channelsForPGG : chr [1:2] "FITC.A" "PerCP.A"
#> $ dV_channelBoundaries : num [1:4] 1250 4000 0 4000
#> $ dV_doRecalcToVolume : logi TRUE
#> $ dV_volumeFactor : num 1e+06
#> $ dV_volumeUnit : chr "ml"
#> $ dV_resolution : num 220
#> $ dV_cutoff_raw : num 10
#> $ dV_cutoff_Vol : num 125
#> $ dV_cutoff_apply : logi TRUE
#> $ dV_ignoreEdgePercent : logi FALSE
#> $ dV_doSmooth : logi TRUE
#> $ dV_smooth_n : num 11
#> $ dV_smooth_p : num 5
#> $ dV_charBeforeFlscNr : chr "flsc"
#> $ dD_useDictionary : logi TRUE
#> $ dD_dict_name : chr "dictionary"
#> $ dD_dict_type : chr "xlsx"
#> $ dD_elementSep : chr ":"
#> $ dD_groupSep : chr ";"
#> $ dD_classVarPrefix : chr "C_"
#> $ dD_numericVarPrefix : chr "Y_"
#> $ dG_locatorLine : chr "darkgreen"
#> $ dG_locatorLineWidth : num 1.4
#> $ dG_gateShowColor : chr "violet"
#> $ dG_pdf_height : num 10
#> $ dG_pdf_width : num 14
#> $ dG_nrBins : num 128
#> $ dG_nonFluorescenceChar: chr [1:2] "FSC.A" "SSC.A"
#> $ dG_alphaForLegends : num 200
#> $ dG_RcolorBrewerPal : chr "Dark2"
#> $ last : num 0