| ggcyto.flowSet {ggcyto} | R Documentation |
Create a new ggcyto plot from a flowSet
## S3 method for class 'flowSet' ggcyto(data, mapping, filter = NULL, ...) ## S3 method for class 'ncdfFlowList' ggcyto(data, ...)
data |
default flowSet for plot |
mapping |
default list of aesthetic mappings (these can be colour, size, shape, line type – see individual geom functions for more details) |
filter |
a flowcore gate object or a function that takes flowSet and channels as input and returns a data-dependent flowcore gate The gate is used to filter the flow data before it is plotted. |
... |
ignored |
a ggcyto_GatingSet object which is a subclass of ggcyto class.
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]]
# 1d histogram/densityplot
p <- ggcyto(fs, aes(x = `FSC-H`))
#facet_wrap(~name)` is used automatically
p1 <- p + geom_histogram()
p1
#overwriting the default faceeting
p1 + facet_grid(Patient~Visit)
#display density
p + geom_density()
#you can use ggjoy package to display stacked density plot
require(ggjoy)
#stack by fcs file ('name')
p + geom_joy(aes(y = name)) + facet_null() #facet_null is used to remove the default facet_wrap (by 'name' column)
#or to stack by Visit and facet by patient
p + geom_joy(aes(y = Visit)) + facet_grid(~Patient)
# 2d scatter/dot plot
p <- ggcyto(fs, aes(x = `FSC-H`, y = `SSC-H`))
p <- p + geom_hex(bins = 128)
p