View source: R/cyto_gate-helpers.R
cyto_gate_edit | R Documentation |
Edit Existing Gate(s).
cyto_gate_edit(
x,
parent = NULL,
alias = NULL,
channels = NULL,
type = NULL,
gatingTemplate = NULL,
overlay = NA,
group_by = "all",
select = NULL,
negate = FALSE,
display = 25000,
axis = "x",
label = TRUE,
plot = TRUE,
popup = TRUE,
axes_limits = "machine",
gate_point_shape = 16,
gate_point_size = 1,
gate_point_col = "red",
gate_point_col_alpha = 1,
gate_line_type = 1,
gate_line_width = 2.5,
gate_line_col = "red",
gate_line_col_alpha = 1,
...
)
x |
an object of class |
parent |
name of the parental population. |
alias |
name(s) of the gate to edit (e.g. "Single Cells"). |
channels |
name(s) of the channel(s) used to construct the gate(s). This
argument is not necessary but is included to allow conversion of
|
type |
vector of gate type names used to construct the gates. Multiple
|
gatingTemplate |
name of the |
overlay |
name(s) of the populations to overlay or a |
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 gs to use for plotting. |
negate |
logical indicating whether a gatingTemplate entry should be made for the negated population (i.e. all events outside the constructed gates), set to FALSE by default. If negate is set to TRUE, a name for the negated population MUST be supplied at the end of the alias argument. |
display |
fraction or number of events to display in the plot during the gating process, set to 25 000 events by default. |
axis |
indicates whether the |
label |
logical indicating whether to include
|
plot |
logical indicating whether a plot should be drawn, set to
|
popup |
logical indicating whether the plot should be constructed in a pop-up window, set to TRUE by default. |
axes_limits |
options include |
gate_point_shape |
shape to use for selected gate points, set to
|
gate_point_size |
numeric to control the size of the selected gate points, set to 1 by default. |
gate_point_col |
colour to use for the selected gate points, set to "red" by default. |
gate_point_col_alpha |
numeric [0,1] to control the transparency of the selected gate points, set to 1 by default to use solid colours. |
gate_line_type |
integer [0,6] to control the line type of gates, set to
|
gate_line_width |
numeric to control the line width(s) of gates, set to
|
gate_line_col |
colour to use for gates, set to |
gate_line_col_alpha |
numeric [0,1] to control the transparency of the selected gate lines, set to 1 by default to use solid colours. |
... |
additional arguments for |
an object of class GatingSet
with edited gate applied, as well
as gatingTemplate file with edited gate saved.
Dillon Hammill, Dillon.Hammill@anu.edu.au
## Not run:
library(CytoExploreRData)
# Load in samples
fs <- Activation
gs <- GatingSet(fs)
# Apply compensation
gs <- cyto_compensate(gs)
# Transform fluorescent channels
gs <- cyto_transform(gs)
# Gate using cyto_gate_draw
gt <- Activation_gatingTemplate
gt_gating(gt, gs)
# Edit CD4 T Cells Gate - replace gatingTemplate name
cyto_gate_edit(gs,
parent = "T Cells",
alias = "CD4 T Cells",
gatingTemplate = "gatingTemplate.csv"
)
## End(Not run)
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