cytobank_to_gatingset {CytoML} | R Documentation |
cytobank_experiment
object) into GatingSetA wrapper that parses the gatingML and FCS files (or cytobank_experiment
object) into GatingSet
## Default S3 method: cytobank_to_gatingset(x, FCS, trans = NULL, ...) ## S3 method for class 'cytobank_experiment' cytobank_to_gatingset(x, panel_id = 1, ...)
x |
the cytobank_experiment object or the full path of gatingML file |
FCS |
FCS files to be loaded |
trans |
a 'transfomerList' object to override the transformations from gatingML files. it is typically used by 'cytobank_experiment' parser(i.e. 'cytobank_to_gatingset.cytobank_experiment') to use the scales info recorded in yaml file. |
... |
other arguments |
panel_id |
select panel to parse |
a GatingSet
## Not run: acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML") ce <- open_cytobank_experiment(acsfile) xmlfile <- ce$gatingML fcsFiles <- list.files(ce$fcsdir, full.names = TRUE) gs <<- cytobank_to_gatingset(xmlfile, fcsFiles) library(ggcyto) autoplot(gs[[1]]) ## End(Not run)