stat_position: Compute the positions of the population statistics based on...

In RGLab/ggcyto: Visualize Cytometry data with ggplot

Compute the positions of the population statistics based on the geometic gate centroid for a ggcyto plot.

Description

It is usually not called directly by user but mainly used by compute_stats function (which is called by ggcyto add method when geom_states layer is added).

Usage

stat_position(gate, ...)

## S3 method for class 'filter'
stat_position(
  gate,
  negated = FALSE,
  adjust = 0.5,
  location = "gate",
  data_range = NULL,
  limits = NULL,
  ...
)

Arguments

gate	a flowCore filter
...	other arguments
negated	logical indicating whether position needs to be moved to negative side of gate
adjust	see details
location	see details
data_range	a two-row data.frame representing the actual data range. Each column is a a range for a specific channel. First row is min, Second row is max.
limits	used to fix the gate range

Details

Specifying location for statistical annotation

The adjust and location arguments allow for a few different ways to adjust the location of the statistical annotation for a gate on a ggcyto plot. The valid values for location are "gate" (default), "data", "plot", and "fixed".

Relative location

If location is not "fixed", the starting position of the annotation will be determined with respect to a rectangular window whose bounds are determined in the following way:

• For location = "gate", the window will be set by the range of the data in the gate

• For location = "data", the window will be set by the range of values in all of the data on the plot (provided by data_range)

• For location = "plot", the window will be set by the axis limits of the plot (adjusted by ggcyto_par_set)

This starting position can then be adjusted by passing values in a vector to the adjust parameter, where they will be interpreted as relative proportions of the window dimension, where 0.0 represents the lower bound of the dimension and 1.0 represents the upper bound. So, for a 2-D plot, adjust=c(0,0) places the annotation at the lower left corner of this window and adjust=c(1,1) places it at the upper right corner.

As another example, for a 2-D gate, if location = "gate" and adjust=c(0.25, 0.75), the statistical annotation will be placed 1/4 of the way across the x-range of the gate and 3/4 of the way across the y-range of the gate.

The adjust argument will also accept values less than 0.0 or greater than 1.0. This can be an easy way to simply move the annotation outside of a gate so it does not obstruct the view of the data within. For example, location == "gate" and adjust=c(-0.2, 1.2) will move the annotation outside of the upper left corner of the gate range.

Fixed location

If location = "fixed", the numeric vector passed to adjust will be interpreted as values on the data scales of the plot to provide an explicit location for the annotation.

For example, if the annotation should be at the location 3000, 5000 on the plot, that could be done with location="fixed" and adjust = c(3000,5000).

Default

The default behavior if no values are provided to location or adjust will be to place the annotation at the center of the range of the data in the gate.

Value

a data.table of gate centroid coordinates

Examples

data(GvHD)
fs <- GvHD[1:4]
rect.g <- rectangleGate(list("FSC-H" =  c(300,500), "SSC-H" = c(50,200)))
rect.gates <- sapply(sampleNames(fs), function(sn)rect.g)
stat_position(rect.gates)

RGLab/ggcyto documentation built on March 3, 2024, 6:23 p.m.