Description Usage Arguments Author(s) Examples
Overlay Points on cyto_plot - list Method
1 2 3 | ## S4 method for signature 'list'
cyto_plot_overlay(x, channels, point_shape = ".",
point_size = 2, point_col = "black", point_alpha = 1)
|
x |
list of |
channels |
channels used to construct the existing cyto_plot. |
point_shape |
point character to use for points, set to "." by default to maximise plotting speed. |
point_size |
numeric specifying the degree of character expansion for points, set to 2 by default. |
point_col |
colours to use for points, set to |
point_alpha |
numeric [0,1] used to control colour transparency, set to 1 by default to remove transparency. |
Dillon Hammill, Dillon.Hammill@anu.edu.au
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(gs))
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"),
axes_trans = trans
)
# Overlay CD4 T Cells & Dendritic Cells
cyto_plot_overlay(list(
getData(gs, "CD4 T Cells")[[4]],
getData(gs, "Dendritic Cells")[[4]]
),
channels = c("APC-Cy7-A", "PE-A"),
point_col = c("magenta", "red")
)
|
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