| autoplot.flowSet {ggcyto} | R Documentation |
Overloaded autoplot methods for the cytometry data structure: flowFrame or flowSet, Gatinghierarchy, GatingSet. It plots the cytometry data with geom_histogram, geom_density or geom_hex. When autoplot a GatingSet/Gatinghierarchy, the second argument should be a gate or population node. And the dimensions(channels/markers) are deduced from the gate dimensions.
## S3 method for class 'flowSet'
autoplot(object, x, y = NULL, bins = 30, ...)
## S3 method for class 'ncdfFlowList'
autoplot(object, ...)
## S3 method for class 'flowFrame'
autoplot(object, x, ...)
## S3 method for class 'GatingSetList'
autoplot(object, ...)
## S3 method for class 'GatingSet'
autoplot(object, gate, x = NULL, y = "SSC-A",
bins = 30, axis_inverse_trans = TRUE, ...)
## S3 method for class 'GatingHierarchy'
autoplot(object, gate, y = "SSC-A",
bool = FALSE, arrange.main = sampleNames(object), arrange = TRUE,
merge = TRUE, projections = list(), strip.text = c("parent",
"gate"), path = "auto", ...)
object |
The data source. A core cytometry data structure. A flowFrame, flowSet, GatingSet or GatingHierarchy object |
x |
define the x dimension of the plot (not used when object is a GatingSet). When object is a flowFrame, it can be missing, which plots 1d density plot on all the channels. |
y |
define the y dimension of the plot. Default is NULL, which means 1d densityplot. |
bins |
passed to geom_hex |
... |
other arguments passed to ggplot |
gate |
the gate to be plotted |
axis_inverse_trans |
logical flag indicating whether to add axis_x_inverse_trans and axis_x_inverse_trans layers. |
bool |
whether to plot boolean gates |
arrange.main |
the main title of the arranged plots |
arrange |
whether to use arrangeGrob to put multiple plots in the same page |
merge |
wehther to merge multiple gates into the same panel when they share the same parent and projections |
projections |
a list of customized projections |
strip.text |
either "parent" (the parent population name) or "gate "(the gate name). The latter usually is used when merge is FALSE |
path |
the gating path format (passed to getNodes) |
a ggcyto object
library(flowCore)
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]]
#1d- density plot
autoplot(fs, x = "SSC-H")
#1d- density plot on all channels
autoplot(fs[[1]])
#2d plot: default geom_hex plot
autoplot(fs, x = 'FSC-H', y ='SSC-H')
#autplot for GatingSet
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
autoplot(gs, "CD3+")
#display axis values in transformed scale
autoplot(gs, "CD3+", axis_inverse_trans = FALSE)
#autplot for GatingHierarchy
gh <- gs[[1]]
autoplot(gh) # by default the strip.text shows the parent population
#To display the gate name
#autoplot(gh , strip.text = "gate")