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.
1 2 3 4 5 |
x |
a |
gates |
an object of class |
trans |
object of class
|
channels |
a vector indicating the fluorescent channel(s) to be used for gating. |
text |
the name of the gated population, set to NA by default to only include percent in labels. |
stat |
indicates the type of statistic to include in the label, can be
either |
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 |
add a boxed text label to cyto_plot.
Dillon Hammill (Dillon.Hammill@anu.edu.au)
cyto_plot_label,flowFrame,rectangleGate-method
cyto_plot_label,flowFrame,polygonGate-method
cyto_plot_label,flowFrame,ellipsoidGate-method
cyto_plot_label,flowFrame,list-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 32 33 34 35 36 37 38 39 40 41 | 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 = "Live Cells",
channels = c("APC-Cy7-A", "PE-A")
)
# T Cells & Dendritic Cells gates
gts <- filters(list(getGate(gs, "T Cells")[[1]],
getGate(gs, "Dendritic Cells")[[1]]))
cyto_plot_gate(gts,
channels = c("APC-Cy7-A", "PE-A"),
gate_line_col = c("red", "black")
)
# Labels
cyto_plot_label(getData(gs, "Live Cells")[[4]],
gates = gts,
trans = trans,
channels = c("APC-Cy7-A", "PE-A"),
text = c("T Cells", "Dendritic Cells"),
stat = "freq",
text_col = c("green4", "purple"),
text_size = 1.2,
box_alpha = 1
)
|
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