Plot Expression Profile in All Fluorescent Channels - flowSet Method

Plot Expression Profile in All Fluorescent Channels - flowSet Method

# S4 method for flowSet
cyto_plot_profile(x, channels = NULL,
  group_by = FALSE, axes_trans = NULL, title = NA,
  density_stack = 0.5, ...)

Arguments

x	object of class flowSet.
channels	a vector channels to use to construct the plots, set to all channels by default.
group_by	a vector of pData variables to sort and merge samples into groups, set to FALSE by default to prevent merging. To merge all samples set this argument to "all".
axes_trans	object of class transformList or transformerList generated by estimateLogicle which was used to transform the fluorescent channels of the supplied flowFrame. This transform object will be used internally to ensure axes labels of the plot are appropriately transformed. The transform object will NOT be applied to the flowFrame internally and should be applied to the flowFrame prior to plotting.
title	a title for the plots, set to the file name of x by default.
density_stack	numeric [0,1] indicating the degree of offset for overlaid populations, set to 0.5 by default.
...	additional arguments passed to cyto_plot,flowFrame-method.

See also

cyto_plot,flowFrame-method

cyto_plot_profile,flowFrame-method

cyto_plot_profile,GatingSet-method

Examples

library(CytoRSuiteData)

# Load in samples
fs <- Activation
gs <- GatingSet(fs)
#> .
#> .
#> .
#> .
#> done!

# Apply compensation
gs <- compensate(gs, fs[[1]]@description$SPILL)

# Transform fluorescent channels
trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
gs <- transform(gs, trans)

# Gate using gate_draw
gt <- Activation_gatingTemplate
gating(gt, gs)
#> Preprocessing for 'Cells'
#> Gating for 'Cells'
#> done.
#> Preprocessing for 'Single Cells'
#> Gating for 'Single Cells'
#> done.
#> Preprocessing for 'Live Cells'
#> Gating for 'Live Cells'
#> done.
#> Preprocessing for 'Dendritic Cells'
#> Gating for 'Dendritic Cells'
#> done.
#> Preprocessing for 'T Cells'
#> Gating for 'T Cells'
#> done.
#> Preprocessing for 'CD8 T Cells'
#> Gating for 'CD8 T Cells'
#> done.
#> Preprocessing for 'CD69+ CD8 T Cells'
#> Gating for 'CD69+ CD8 T Cells'
#> done.
#> Preprocessing for 'CD4 T Cells'
#> Gating for 'CD4 T Cells'
#> done.
#> Preprocessing for 'CD69+ CD4 T Cells'
#> Gating for 'CD69+ CD4 T Cells'
#> done.
#> finished.

# Plot expression profile in all channels
cyto_plot_profile(getData(gs, "T Cells"),
  axes_trans = trans
)