getProp,GatingHierarchy,character-method {flowWorkspace} | R Documentation |
getProp calculates the population proportion (events in the gate / events in the parent population) associated with a node in the GatingHierarchy
.
getPopStats is more useful than getPop. Returns a table of population statistics for all populations in a GatingHierarchy
/GatingSet
. Includes the xml counts, openCyto counts and frequencies.
getTotal returns the total number of events in the gate defined in the GatingHierarchy object
## S4 method for signature 'GatingHierarchy,character' getProp(x, y, xml = FALSE) ## S4 method for signature 'GatingHierarchy,character' getTotal(x, y, xml = FALSE) ## S4 method for signature 'GatingHierarchy' getPopStats(x, path = "auto", ...) ## S4 method for signature 'GatingSet' getPopStats(x, statistic = c("freq", "count"), xml = FALSE, subpopulations = NULL, format = c("long", "wide"), path = "full", ...) ## S4 method for signature 'GatingSetList' getPopStats(x, format = c("long", "wide"), ...)
x |
A |
y |
|
xml |
|
path |
|
... |
Additional arguments passed to getNodes |
statistic |
|
subpopulations |
|
format |
|
getPopStats returns a table population statistics for all populations in the gating hierarchy. The output is useful for verifying that the import was successful, if the xml and openCyto derived counts don't differ much (i.e. if they have a small coefficient of variation.) for a GatingSet, returns a matrix of proportions for all populations and all samples
getProp returns the proportion of cells in the gate, relative to its parent.
getTotal returns the total number of events included in this gate. The contents of "thisTot" variable in the "metadata" environment of the nodeData
element associated with the gating tree and gate / population.
getPopStats returns a data.frame
with columns for the population name, xml derived counts, openCyto derived counts, and the population proportions (relative to their parent pouplation).
getProp returns a population frequency numeric
.
getTotal returns a numeric
value of the total number of elements in the population.
## Not run: #gh is a GatingHierarchy getPopStats(gh); #proportion for the fifth population getProp(gh,getNodes(gh)[5]) getTotal(gh,getNodes(gh,tsort=T)[5]) #gs is a GatingSet getPopStats(gs) #optionally output in long format as a data.table getPopStats(gs, format = "long", path = "auto") #only get stats for a subset of populations getPopStats(gs, format = "long", subpopulations = getNodes(gs)[4:6]) ## End(Not run)