Add labels to cyto_plot

Interactively label existing plots with boxed labels containing text and statistics. cyto_plot_label can only label the last plot and can only add labels on a per sample basis (i.e. single layer only). Locations for each label must be manually selected. More complex labelling can be acheived directly through cyto_plot.

# S3 method for GatingHierarchy
cyto_plot_label(
  x,
  parent,
  alias = NA,
  channels = NULL,
  display = 1,
  gate = NA,
  negate = NA,
  label_text,
  label_stat,
  label_text_x = NA,
  label_text_y = NA,
  label_text_font = 2,
  label_text_size = 0.8,
  label_text_col = "black",
  label_fill = "white",
  label_fill_alpha = 0.6,
  density_smooth = 0.6,
  ...
)

# S3 method for flowFrame
cyto_plot_label(
  x,
  channels = NULL,
  trans = NA,
  display = 1,
  gate = NA,
  negate = FALSE,
  label_text = NA,
  label_stat = NA,
  label_text_x = NA,
  label_text_y = NA,
  label_text_font = 2,
  label_text_size = 0.8,
  label_text_col = "black",
  label_fill = "white",
  label_fill_alpha = 0.6,
  density_smooth = 0.6,
  ...
)

Arguments

x	object of class flowFrame.
parent	name of the parent population to extract when a GatingHierarchy object is supplied.
alias	name of teh gated populations to label when a GatingHierarchy object is supplied. This is equivalent to the gate argument for flowFrame objects.
channels	a vector indicating the fluorescent channel(s) to be used for gating.
display	numeric [0,1] to control the percentage of events to be plotted. Specifying a value for display can substantial improve plotting speed for less powerful machines.
gate	object of class rectangleGate, polygonGate, ellipsoidGate, quadGate, "list" or filters.
negate	logical indicating whether a label should be included for the neagted population (i.e. events outside the gate). Set to FALSE by default to only calculate statistics for events within the gate.
label_text	character string to include in the label above the statistic (e.g. population name(s)).
label_stat	indicates the type of statistic to include in the label, can be either code"count", "median", "mean", "mode", "geo mean" or "CV". Only count and percent statistics are supported for 2D plots.
label_text_x	vector containing the x co-ordinates for the plot labels. Label positions can be interactively selected if no co-ordinates are manually supplied.
label_text_y	vector containing the x co-ordinates for the plot labels. Label positions can be interactively selected if no co-ordinates are manually supplied.
label_text_font	integer [1,2,3,4] passed to text to alter the font, set to 2 by default for a bold font.
label_text_size	numeric character expansion used to control the size of the text in the labels, set to 0.8 by default. See ?text for details.
label_text_col	specify text colour in label for each gate, defaults to "black" for all gates.
label_fill	fill colour to use for labels, set to "white" by default.
label_fill_alpha	numeric [0,1] controls the transparency of the fill colour, set to 0.6 by default.
density_smooth	smoothing parameter passed to density to adjust kernel density for mode calculation.
...	not in use.
trans	object of class transformerList which was used to transform the fluorescent channels of the supplied flowFrame.

Value

add a boxed text label to an existing cyto_plot.

Author

Dillon Hammill (Dillon.Hammill@anu.edu.au)

Examples

library(CytoExploreRData)

# Load in samples
fs <- Activation
gs <- GatingSet(fs)

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

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

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

# Plot
cyto_plot(gs[[32]],
  parent = "CD4 T Cells",
  channels = c("CD69")
)

# Label - median fluorescent intensity
cyto_plot_label(cyto_extract(gs, "CD4 T Cells")[[32]],
  channels = "CD69",
  label_stat = "median",
  label_text = "MedFI",
  trans = trans,
  label_text_x = 3,
  label_text_y = 50
)