Plot flowstate data

Plot flowstate data

Usage

# S3 method for class 'flowstate'
plot(x, ..., bins = 200, limits = NULL, sample.n = NULL)

Arguments

x

A flowstate object as returned from read.flowstate.

...

... aes arguments (unquoted variables); essentially x and y. If a z aesthetic is defined, the plot will switch to stat_summary_hex, using this defined third variable as a 'color-by'.

bins

geom_hex argument; numeric giving the number of bins in both vertical and horizontal directions.

limits

continuous_scale argument.

sample.n

Numeric (length 1); if defined, will randomly sample events from [[data]].

Value

A ggplot object.

Examples

fcs.file.paths <- system.file("extdata", package = "flowstate") |>
list.files(full.names = TRUE, pattern = "BLOCK.*.fcs")

#read all .fcs files as flowstate objects; concatenate into a single object
fs <- read.flowstate(
  fcs.file.paths,
  colnames.type="S",
  concatenate = TRUE
)
#> COVAIL_002_CYTOKINE_BLOCK1_1.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_2.fcs --> flowstate
#> COVAIL_002_CYTOKINE_BLOCK1_3.fcs --> flowstate
#> Concatenating 'flowstate.ojects'...

#transform
flowstate.transform(fs,c('CD3','CD4','CD8','Viability'))
#> flowstate.object --> transforming...

#plot title
no.fill.legend <- ggplot2::guides(fill = 'none')
.title1 <- paste("Batch:",fs$keywords[,unique(`$PROJ`)])
.title2 <- paste(
  "Instrument Serial#:",
  fs$keywords[,paste(.(unique(`$CYT`),unique(`$CYTSN`)),collapse = " ")]
)
.title <- paste(.title1,.title2,sep = "\n")
.title <- ggplot2::labs(title = .title)

#plot: two variables
plot(fs,CD3,Viability) + no.fill.legend + .title
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.

plot(fs,FSC_A,SSC_A) + no.fill.legend + .title
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.


#plot: two variables; facet by sample.id
plot(fs,CD4,CD8) + no.fill.legend + .title + ggplot2::facet_wrap(~sample.id)
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.
#> Warning: Computation failed in `stat_binhex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_bin_hex()`.


#plot: three variables; color-by
plot(fs,FSC_A,SSC_A,z=Viability,bins=100,limits=c(0,3)) + .title
#> Warning: Computation failed in `stat_summary_hex()`.
#> Caused by error in `compute_group()`:
#> ! The package "hexbin" is required for `stat_summary_hex()`.