## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set() ## ----------------------------------------------------------------------------- library(CytoML) dataDir <- system.file("extdata",package="flowWorkspaceData") wsfile <- list.files(dataDir, pattern="manual.xml",full=TRUE) ws <- open_flowjo_xml(wsfile) ws ## ----------------------------------------------------------------------------- tail(fj_ws_get_sample_groups(ws)) ## ----------------------------------------------------------------------------- fj_ws_get_samples(ws, group_id = 5) ## ----------------------------------------------------------------------------- fj_ws_get_keywords(ws, 28)[1:5] ## ----eval=FALSE--------------------------------------------------------------- # gs <- flowjo_to_gatingset(ws, name = "T-cell") ## ----eval=FALSE--------------------------------------------------------------- # gs <- flowjo_to_gatingset(ws, name = 4) ## ----eval=FALSE--------------------------------------------------------------- # gs <- flowjo_to_gatingset(ws, name = 4, path = dataDir) ## ----------------------------------------------------------------------------- gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE) gs ## ----------------------------------------------------------------------------- suppressMessages(library(flowWorkspace)) plot(gs) ## ----------------------------------------------------------------------------- gs_pop_get_gate(gs, "CD3+") ## ----------------------------------------------------------------------------- gs_get_compensations(gs)[1] ## ----------------------------------------------------------------------------- gh_get_transformations(gs[[1]], channel = "B710-A") ## ----------------------------------------------------------------------------- head(gs_pop_get_stats(gs, xml = TRUE)) ## ----error=TRUE--------------------------------------------------------------- gs_pop_get_data(gs) ## ----------------------------------------------------------------------------- sampleNames(gs) ## ----------------------------------------------------------------------------- gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL) sampleNames(gs) ## ----------------------------------------------------------------------------- gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = c("$TOT", "EXPERIMENT NAME")) sampleNames(gs) ## ----------------------------------------------------------------------------- gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.sampleID = TRUE) sampleNames(gs) ## ----------------------------------------------------------------------------- pData(gs) ## ----------------------------------------------------------------------------- gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL, keywords = c("EXPERIMENT NAME", "TUBE NAME")) pData(gs) ## ----------------------------------------------------------------------------- gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL, subset = 1:2) sampleNames(gs) ## ----eval=FALSE--------------------------------------------------------------- # gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL, subset = c("CytoTrol_CytoTrol_3.fcs")) # sampleNames(gs) ## ----------------------------------------------------------------------------- gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE, additional.keys = NULL , subset = `EXPERIMENT NAME` == "C2_Tcell" , keywords = c("EXPERIMENT NAME") ) pData(gs) ## ----eval=FALSE--------------------------------------------------------------- # gs <- flowjo_to_gatingset(ws, name = 4, mc.cores = 4) ## ----echo=FALSE--------------------------------------------------------------- is_local <- dir.exists("~/rglab/workspace/CytoML/wsTestSuite") ## ----echo=FALSE, eval=is_local------------------------------------------------ # path <- "~/rglab/workspace/CytoML/wsTestSuite" # thisPath <- file.path(path, "searchRefNode") # wsFile <- file.path(thisPath, "2583-Y-MAL067-FJ.xml") # ws <- open_flowjo_xml(wsFile) ## ----eval=is_local------------------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name="Samples", subset = "1379326.fcs", execute = FALSE) # nodes <- gs_get_pop_paths(gs) # length(nodes) # plot(gs, "3+") ## ----eval=is_local------------------------------------------------------------ # tail(nodes, 10) ## ----eval=is_local------------------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name="Samples", subset = "1379326.fcs", leaf.bool = F) # gs_pop_get_stats(gs) ## ----eval=is_local------------------------------------------------------------ # recompute(gs) # gs_pop_get_stats(gs) ## ----echo=FALSE, eval=is_local------------------------------------------------ # wsFile <- file.path(path, "bypassfaultynode.xml") # ws <- open_flowjo_xml(wsFile) # dataDir <- file.path(path,"Cytotrol/NHLBI/Tcell/") ## ----error=TRUE, eval=is_local------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name = 4, path = dataDir, subset = 1) ## ----eval=is_local------------------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name = 4, path = dataDir, execute = FALSE) # plot(gs) # gs_pop_get_gate(gs, "CD4")[[1]] ## ----eval=is_local------------------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name = 4, path = dataDir, subset = 1, skip_faulty_gate = TRUE) # head(gs_pop_get_stats(gs)) ## ----echo=FALSE, eval=is_local------------------------------------------------ # wsFile <- file.path(path, "no-gate.wsp") # ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode') ## ----error=TRUE, eval=is_local------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name = 1, path = dataDir) ## ----eval=is_local------------------------------------------------------------ # fj_ws_get_samples(ws) ## ----eval=is_local------------------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name = 1, path = dataDir, include_empty_tree = TRUE) # range(gs_cyto_data(gs)[[1]]) ## ----echo=FALSE, eval=is_local------------------------------------------------ # wsFile <- file.path(path, "logicle.wsp") # ws <- open_flowjo_xml(wsFile) # dataDir <- system.file("extdata", package = "flowCore") ## ----error=TRUE, eval=is_local------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name = 1, path = dataDir, additional.keys = NULL) ## ----eval=is_local------------------------------------------------------------ # gs <- flowjo_to_gatingset(ws, name = 1, path = dataDir, additional.keys = NULL, fcs_file_extension = ".B08") # sampleNames(gs)