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
if (FALSE) { 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" ) }