CytoML
provides flowjo_to_gatingset
function to parse FlowJo
workspace (xml
or
wsp
file) and FCS files into a self-contained
GatingSet
object, which captures the entire analysis
recorded in flowJo, include compensation
,
transformation
and gating
.
library(CytoML)
dataDir <- system.file("extdata",package="flowWorkspaceData")
wsfile <- list.files(dataDir, pattern="manual.xml",full=TRUE)
ws <- open_flowjo_xml(wsfile)
ws
## File location: /home/biocbuild/bbs-3.21-bioc/R/site-library/flowWorkspaceData/extdata/manual.xml
##
## Groups in Workspace
## Name Num.Samples
## 1 All Samples 45
## 2 B-cell 4
## 3 DC 4
## 4 T-cell 4
## 5 Thelper 4
## 6 Treg 4
Once opened, sample group information can be retrieved
tail(fj_ws_get_sample_groups(ws))
## groupName groupID sampleID
## 60 Thelper 4 30
## 61 Thelper 4 31
## 62 Treg 5 37
## 63 Treg 5 38
## 64 Treg 5 39
## 65 Treg 5 40
And sample information for a given group
fj_ws_get_samples(ws, group_id = 5)
## sampleID name count pop.counts
## 1 28 CytoTrol_CytoTrol_1.fcs 136304 23
## 2 29 CytoTrol_CytoTrol_2.fcs 115827 23
## 3 30 CytoTrol_CytoTrol_3.fcs 123170 23
## 4 31 CytoTrol_CytoTrol_4.fcs 114802 23
keywords recorded in xml for a given sample
fj_ws_get_keywords(ws, 28)[1:5]
## $`$BEGINANALYSIS`
## [1] "0"
##
## $`$BEGINDATA`
## [1] "3241"
##
## $`$BEGINSTEXT`
## [1] "0"
##
## $`$BTIM`
## [1] "13:28:46"
##
## $`$BYTEORD`
## [1] "4,3,2,1"
In majority use cases, only two parameters are required to complete the parsing, i.e.
name
: the group to importpath
: the data path of FCS files.name
parameter can be set to the group name displayed
above through flowJo_workspace
APIs.
gs <- flowjo_to_gatingset(ws, name = "T-cell")
name
can also be the numeric index
gs <- flowjo_to_gatingset(ws, name = 4)
As shown above, the path
be omitted if fcs files are
located at the same folder as xml file.
Otherwise, path
is set the actual folder where FCS files
are located. The folder can contain sub-folders and the parser will
recursively look up the directory for FCS files (by matching the file
names, keywords, etc)
gs <- flowjo_to_gatingset(ws, name = 4, path = dataDir)
path
can alternatively be a , which should contain two
columns:‘sampleID’ and ‘file’. It essentially provides hardcoded mapping
between ‘sampleID’ and FCS file (absolute) path to avoid the file system
searching or sample matching process (between the flowJo sample
reference and the FCS files).
However this is rarely needed since auto-searching does pretty accurate and robust matching.
Due to the varieties of FlowJo workspace or FCS file issues, sometime the default setting won’t be sufficient to handle some edge cases, e.g. when the error occurs at specific gate due to the incorrect gate parameters defined in xml , but we want to be able to import the upstream gates that are still useful. Or there is letter case inconsistency for channels used in xml, which will trigger an error by default.
Also there are other features provided by the parser that allow users to speed up the parsing or extract more meta data from either xml or FCS files.
flowjo_to_gatingset
provides more parameters that can be
configured to solve different problems during the parsing. In document
aims to go through these parameters and explore them one by one.
It is possible to only import the gating structure without reading
the FCS data by setting execute
flag to
FALSE
.
gs <- flowjo_to_gatingset(ws, name = 4, execute = FALSE)
gs
## A GatingSet with 4 samples
Gating hierarchy is immediately available
suppressMessages(library(flowWorkspace))
plot(gs)