View source: R/cyto_plot_profile.R
cyto_plot_profile | R Documentation |
Plot expression profile in all channels
## S3 method for class 'GatingSet' cyto_plot_profile( x, parent = NULL, channels = NULL, group_by = NA, select = NULL, axes_trans = NA, layout = NULL, header = NULL, header_text_font = 2, header_text_size = 1, ... ) ## S3 method for class 'GatingHierarchy' cyto_plot_profile( x, parent = NULL, channels = NULL, axes_trans = NA, header = NULL, header_text_font = 2, header_text_size = 1, ... ) ## S3 method for class 'flowSet' cyto_plot_profile( x, channels = NULL, group_by = NA, select = NA, axes_trans = NULL, layout = NULL, header = NULL, header_text_font = 2, header_text_size = 1, density_stack = 0.5, ... ) ## S3 method for class 'flowFrame' cyto_plot_profile( x, channels = NULL, axes_trans = NA, layout = NULL, header = NULL, header_text_font = 2, header_text_size = 1, ... )
x |
object of class |
parent |
name of the population to plot when a |
channels |
a vector channels to use to construct the plots, set to all channels by default. |
group_by |
a vector of experiment variables to sort and merge samples
into groups prior to plotting, set to NA by default to prevent merging.
To merge all samples set this argument to |
select |
designates which samples will be plotted and used for
determining the best location to set the drawn gate(s). Filtering steps
should be comma separated and wrapped in a list. Refer to
|
axes_trans |
object of class
|
layout |
a vector of the length 2 indicating the dimensions of the grid
for plotting |
header |
character string to include in the plot header, set to the sample names by deafult. The header can be removed by setting this argument to NA. |
header_text_font |
numeric indicating the font to use for the header, set to 2 by default for bold font. |
header_text_size |
numeric to control the text size of the header, set to 1 by deafult. |
... |
additional arguments passed to |
density_stack |
numeric [0,1] indicating the degree of offset for 1-D density distributions with overlay, set to 0.5 by default. |
Dillon Hammill (Dillon.Hammill@anu.edu.au)
cyto_plot
# Load in CytoExploreR to access data library(CytoExploreRData) # Load in samples fs <- Activation gs <- GatingSet(fs) # Apply compensation gs <- cyto_compensate(gs, fs[[1]]@description$SPILL) # Transform fluorescent channels gs <- cyto_transform(gs, trans_type = "logicle") # Apply gates gt <- Activation_gatingTemplate gt_gating(gt, gs) # Plot expression profile of T Cells in all channels cyto_plot_profile(gs[1:9], parent = "T Cells" ) # Group samples by Treatment & select highest OVAConc cyto_plot_profile(gs[1:9], parent = "CD4 T Cells", group_by = "Treatment", select = list("OVAConc" = 500), )
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