rggplot2bioconductor

setting x-limits on ggcyto plot doesn't seem to do the trick

I am trying to set the x limits on a ggcyto(ggplot2) plot, but it doesn't seem to work. The x-limit that I set is squished all the way to the right and there is a lot of empty space. Not sure what else to try. I tried setting biexp scale but it looked the same.

library(ggcyto)
library(ggplot2)
library(flowCore)

fs <- read.flowSet(fcs_files, path=(dir_path))


ggcyto(fs[[2]],
              aes(x = "FSC-A", 
              y = "SSC-A")  
              ) + 
  geom_hex(bins = 26) +
  xlab("") +
  ylab("") +
  theme(
    strip.text = element_text(size = 5),
  ) +
  scale_x_continuous(breaks = c(0, 18000), labels = function(x) formatC(x, format="e", digits =1), limits=c(0, 20000))) #+
  #scale_x_flowjo_biexp(maxValue = 20000, widthBasis = -10)

Adding limits=c(0, 20000) gives me this warning: Warning message: Removed 14 rows containing non-finite values (stat_binhex).

plot output

Solution

  • Don't have your data so can't reproduce the weird axis. I would check your data for negative values. Also the ggcyto wrapper has some restrictions on your limits.

    Using an example data below, I set 2 values on the first column "FSC" to be -999, and I get a similar error:

    library(ggcyto)
data(GvHD)
da = GvHD[[1]]
exprs(da)[1:2,1] = -999 
    
ggcyto(da, aes(x = `FSC-H`, y =  `SSC-H`)) +
geom_hex(bins = 50) +
scale_x_continuous(breaks =c(0,800),limits = c(0,2000))

    enter image description here

    And the error:

    Warning message: Removed 2 rows containing non-finite values (stat_binhex).

    If I remove the entries with negative values and also use ggplot2 instead of ggcyto, it works

    da = da[rowMeans(exprs(da[,1:2])>0) == 1,]

ggplot(da,aes(x = `FSC-H`, y =  `SSC-H`)) + 
geom_hex(bins=50) + 
scale_x_continuous(breaks =c(0,800),limits=c(0,1200))+
scale_fill_distiller(palette = "Spectral")

    enter image description here

    In your example, you can try something like:

    da = fs[[2]]
da = da[rowMeans(exprs(da[,c("FSC-A","SSC-A")])>0) == 1,]

ggplot(da,aes(x = `FSC-A`,y = `SSC-A`)) + 
geom_hex(bins = 26) +
scale_x_continuous(breaks = c(0, 18000),limits=c(0, 20000)))