library(ggcyto)
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5:7 & Visit %in% c(5:6))[["name"]]]
fr <- fs[[1]]

1d histogram/densityplot

ggcyto wrapper will construct the ggcyto object that inherits from ggplot class.

p <- ggcyto(fs, aes(x = `FSC-H`)) 
class(p)
## [1] "ggcyto_flowSet"
## attr(,"package")
## [1] "ggcyto"
is(p, "ggplot")
## [1] TRUE

Since only one dimension is specified, we can add any 1d geom layer

p1 <- p + geom_histogram() 
p1

As shown, data is facetted by samples name automatically (i.e facet_wrap(~name)).

We can overwrite the default faceting by any variables that are defined in pData

pData(fs)
##       Patient Visit Days Grade  name
## s5a05       5     5   19     3 s5a05
## s5a06       5     6   26     3 s5a06
## s6a05       6     5   19     3 s6a05
## s6a06       6     6   27     3 s6a06
## s7a05       7     5   21     3 s7a05
## s7a06       7     6   28     3 s7a06
p1 + facet_grid(Patient~Visit)

To display 1d density

p + geom_density()

Fill the same color

p + geom_density(fill = "black")

Fill different colors

ggcyto(fs, aes(x = `FSC-H`, fill = name)) + geom_density(alpha = 0.2)

Or plot in the same panel by using ggplot directly (thus removing the default facetting effect)

ggplot(fs, aes(x = `FSC-H`, fill = name)) + geom_density(alpha = 0.2)

stacked density plot

#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

# 2d hex
p <- ggcyto(fs, aes(x = `FSC-H`, y =  `SSC-H`))
p <- p + geom_hex(bins = 128)
p