gate_flowclust_2d {openCyto} | R Documentation

## Automatic identification of a population of interest via flowClust based on two markers

### Description

We cluster the observations in `fr` into `K` clusters. We set the cutpoint to be the point at which the density between the first and second smallest cluster centroids is minimum.

### Usage

    gate_flowclust_2d(
      fr,
      xChannel,
      yChannel,
      filterId = "",
      K = 2,
      usePrior = "no",
      prior = list(NA),
      trans = 0,
      min.count = -1,
      max.count = -1,
      nstart = 1,
      plot = FALSE,
      target = NULL,
      transitional = FALSE,
      quantile = 0.9,
      translation = 0.25,
      transitional_angle = NULL,
      min = NULL,
      max = NULL,
      ...
    )

### Arguments

`fr` | a `flowFrame` object
`xChannel, yChannel` | `character` specifying channels to be gated on
`filterId` | A `character` string that identifies the filter created.
`K` | the number of clusters to find
`usePrior` | Should we use the Bayesian version of `flowClust`? Answers are "yes", "no", or "vague". The answer is passed along to `flowClust`.
`prior` | list of prior parameters for the Bayesian version of `flowClust`. If `usePrior` is set to `no`, then the list is unused.
`trans, min.count, max.count, nstart` | some flowClust parameters. see `flowClust`
`plot` | a logical value indicating if the fitted mixture model should be plotted. By default, no.
`target` | a numeric vector of length `2` (number of dimensions) containing the location of the cluster of interest. See details.
`transitional` | logical value indicating if a transitional gate should be constructed from the target `flowClust` cluster. By default, no.
`quantile` | the contour level of the target cluster from the `flowClust` fit to construct the gate
`translation` | a numeric value between 0 and 1 used to position a transitional gate if `transitional = TRUE`. This argument is ignored if `transitional = FALSE`. See details
`transitional_angle` | the angle (in radians) of the transitional gate. It is also used to determine which quadrant the final gate resides in. See details. Ignored if `transitional = FALSE`.
`min` | A vector of length 2. Truncate observations less than this minimum value. The first value truncates the `xChannel`, and the second value truncates the `yChannel`. By default, this vector is `NULL` and is ignored.
`max` | A vector of length 2. Truncate observations greater than this maximum value. The first value truncates the `xChannel`, and the second value truncates the `yChannel`. By default, this vector is `NULL` and is ignored.
`...` | additional arguments that are passed to `flowClust`

### Details

The cluster for the population of interest is selected as the one with cluster centroid nearest the `target` in Euclidean distance. By default, the largest cluster (i.e., the cluster with the largest proportion of observations) is selected as the population of interest.

We also provide the option of constructing a `transitional` gate from the selected population of interest. The location of the gate can be controlled with the `translation` argument, which translates the gate along the major axis of the targest cluster as a function of the appropriate chi-squared coefficient. The larger `translation` is, the more gate is shifted in a positive direction. Furthermore, the width of the `transitional` gate can be controlled with the `quantile` argument.

The direction of the transitional gate can be controlled with the `transitional_angle` argument. By default, it is `NULL`, and we use the eigenvector of the `target` cluster that points towards the first quadrant (has positive slope). If `transitional_angle` is specified, we rotate the eigenvectors so that the angle between the x-axis (with the cluster centroid as the origin) and the major eigenvector (i.e., the eigenvector with the larger eigenvalue) is `transitional_angle`. So based on range that the angle falls in, the final rectangleGate will be constructed at the corresponding quadrant. i.e. Clockwise, [0,pi/2] UR, (pi/2, pi] LR, (pi, 3/2 * pi] LL, (3/2 * pi, 2 * pi] UL

### Value

a `polygonGate` object containing the contour (ellipse) for 2D gating.

### Examples

    ## Not run:
     gate <- gate_flowclust_2d(fr, xChannel = "FSC-A", xChannel = "SSC-A", K = 3) # fr is a flowFrame

    ## End(Not run)

[Package openCyto version 2.2.0 Index]