Description Usage Arguments Value Author(s) See Also Examples
cyto_plot_label
takes on a flowFrame
object, population name
text
, channels
and a gate object to construct a text label for
the plot with the population name and frequency. In the absence of a gate,
users can manually specify the label position using the text_x
and
text_y
arguments.
1 2 3 4 5 |
x |
a |
gates |
|
trans |
object of class
|
channels |
a vector indicating the fluorescent channel(s) to be used for gating. |
text |
character string to include in the label above the statistic (e.g. population name(s)). |
stat |
indicates the type of statistic to include in the label, can be
either code"count", |
text_x |
vector containing the x co-ordinates for the plot labels. Set
to |
text_y |
vector containing the x co-ordinates for the plot labels. Set
to |
text_font |
integer [1,2,3,4] passed to |
text_size |
numeric character expansion used to control the size of the
text in the labels, set to |
text_col |
specify text colour in label for each gate, defaults to
|
box_alpha |
numeric [0,1] controls the transparency of the background,
set to |
density_smooth |
smoothing parameter passed to
|
add a boxed text label to cyto_plot.
Dillon Hammill (Dillon.Hammill@anu.edu.au)
cyto_plot_label,flowFrame,polygonGate-method
cyto_plot_label,flowFrame,ellipsoidGate-method
cyto_plot_label,flowFrame,list-method
cyto_plot_label,flowFrame,filters-method
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | library(CytoRSuiteData)
# 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
gating(Activation_gatingTemplate, gs)
# Plot
cyto_plot(gs[[4]],
parent = "T Cells",
channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A")
)
# Labels without gates - position using text_x and text_y
cyto_plot_label(getData(gs, "T Cells")[[4]],
gates = NULL,
channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
trans = trans,
text = c("CD4 T Cells", "CD8 T Cells"),
text_x = c(3.1, 1),
text_y = c(-0.2, 3.2)
)
|
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