Description Usage Arguments Value Author(s) See Also Examples
Manually draw gates around populations for analysis of flow cytometry data.
1 2 3 4 5 |
x |
object of class
|
group_by |
vector of pData column names (e.g. c("Treatment","Concentration") indicating how the samples should be grouped prior to gating, set to the length of x by default to construct a single gate for all samples. If group_by is supplied a different gate will be constructed for each group. |
select |
vector containing the indices of samples within each group to use for plotting. |
parent |
name of the |
alias |
the name(s) of the populations to be gated. If multiple
population names are supplied (e.g. |
channels |
vector of channel names to use for plotting, can be of length 1 for 1-D density histogram or length 2 for 2-D scatter plot. |
type |
vector of gate type names used to construct the gates. Multiple
gate types are supported but should be accompanied with an |
gatingTemplate |
name of |
display |
numeric [0,1] to control the percentage of events to be
plotted. Specifying a value for |
axis |
indicates whether the |
density_smooth |
smoothing factor passed to
|
label |
logical indicating whether to include
|
plot |
logical indicating whether a plot should be drawn, set to
|
... |
additional arguments for |
drawn gates are applied to the
GatingSet
and saved to a
gatingTemplate
.
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 | ## Not run:
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)
# draw gates using gate_draw - add contour lines & overlay control
gate_draw(gs,
parent = "Dendritic Cells",
channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
alias = c("CD8+ DC", "CD4+ DC"),
gatingTemplate = "Example-gatingTemplate.csv",
type = "rectangle",
contour_lines = 15
)
# Constructed gate applied directly to GatingSet
getNodes(gs)
## End(Not run)
|
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