cyto_gate_draw
allows to users to interactive draw gates around
populations which are returned as flowCore
gate objects. The flowFrame
and flowSet methods simply return the constructed gates as a list of
flowCore-compatible gate objects, whilst the GatingSet method automatically
applies the constructed gates to the GatingSet and saves the constructed
gates in an openCyto
gatingTemplate
for future use.
See cyto_gate_edit
, cyto_gate_remove
and
cyto_gate_rename
to manipulate constructed gates and modify
their entries in the gatingTemplate.
# S3 method for GatingSet cyto_gate_draw( x, parent = "root", 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, ... ) # S3 method for flowSet cyto_gate_draw( x, alias = NULL, channels = NULL, type = 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, ... ) # S3 method for flowFrame cyto_gate_draw( x, alias = NULL, channels = NULL, type = NULL, overlay = NA, 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 | |
---|---|
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 |
overlay | name(s) of the populations to overlay or a |
group_by | vector of |
select | designates which samples will be plotted and used for
determining the best location to set the drawn gate(s). Filtering steps
should be comma separated and wrapped in a list. Refer to
|
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 |
flowFrame
and flowSet
methods return a list of flowCore
gate objects per group in group_by, whilst the GatingSet
applies the
constructed gates directly to the GatingSet
and adds appropriate
entries into the specified gatingTemplate
. The GatingSet
method does not return the constructed gates but instead invisibly returns
the gatingTemplate
entries.
Dillon Hammill, Dillon.Hammill@anu.edu.au
if (FALSE) { # Gate drawing requires an interactive R session library(CytoExploreRData) # 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 cyto_gate_draw gt_gating(Activation_gatingTemplate, gs) # draw gates using cyto_gate_draw cyto_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 cyto_nodes(gs) }