![]() Exporting your data in CSV – Want to crunch the raw numbers in a spreadsheet or statistical package? Try creating this text file format that is easily digested by the most finicky parsers.You can export an entire file and select the number of events you want in the new file, or you can export a gated subset and get a new file with just the events in that gated region. Just right click a file in the workspace and choose Export.Exporting new FCS files – Need to clean up data or reduce file size? Try exporting a subset of your data file into a fresh new FCS file and reimport into FlowJo.The default format for many areas’ export actions can be set in File Format Preferences. Click on the links below for more detailed information about export options for each area. The interface areas of FlowJo that have export options are listed below, along with their relevant export formats. From almost every interface of the program there is a way to get your sample data, plots, or statistics out of FlowJo for use in spreadsheets, graphics programs, or almost any secondary software package. # CytoTrol_CytoTrol_4.fcs CytoTrol_CytoTrol_4.Getting the good stuff inside FlowJo out for other uses!įlowJo makes exporting your analyses quick and easy. # CytoTrol_CytoTrol_3.fcs CytoTrol_CytoTrol_3.fcs C2_Tcell # CytoTrol_CytoTrol_2.fcs CytoTrol_CytoTrol_2.fcs C2_Tcell # CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs C2_Tcell , subset = `EXPERIMENT NAME` = "C2_Tcell" gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL Note that the columns referred by the expression must also be explicitly specified in ‘keywords’ argument, which we will cover in the later sections.Į.g. Or an that is similar to the one passed to ‘base::subset’ function to filter a ame. gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL, subset = c("CytoTrol_CytoTrol_3.fcs")) Or the vector of sample (FCS) names, e.g. SampleNames(gs) # "CytoTrol_CytoTrol_1.fcs" "CytoTrol_CytoTrol_2.fcs" gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL, subset = 1:2) Subset argument takes numeric indies, e.g. Sometime it is useful to only select a small subset of samples to import to quickly test or review the content of gating tree instead of waiting for the entire data set to be completed, which could take longer time if the total number of samples is big. gs_pop_get_data(gs) # Error: gate is not parsed! Otherwise it will display the value computed from FCS file, which will be NA in this case since we didn’t load FCS files.Īpparently, it is very fast to only import xml, but data won’t be available for retrieving. Note that xml flag needs to be set in order to tell it to return the stats from xml file. # stop("'deriv' must be between 0 and 3")Īnd stats head(gs_pop_get_stats(gs, xml = TRUE)) # sample pop count Transformations gh_get_transformations(gs], channel = "B710-A") # function (x, deriv = 0) # Compensation object 'defaultCompensation': # Ellipsoid gate 'CD3+' in dimensions and SSC-AĬompensations gs_get_compensations(gs) # $CytoTrol_CytoTrol_1.fcs_119531 It is possible to only import the gating structure without reading the FCS data by setting execute flag to FALSE.
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