View source: R/cyto_gate_draw.R
cyto_gate_draw | R Documentation |
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 class '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 class '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 class '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 |
object of class |
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
cyto_plot
cyto_gate_edit
cyto_gate_remove
cyto_gate_rename
## Not run:
# 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)
## End(Not run)
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