stat_position {ggcyto} | R Documentation

## 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)

[Package ggcyto version 1.22.0 Index]