imbalance_score {condiments} | R Documentation

## Imbalance Score

### Description

Compute a imbalance score to show whether nearby cells have the same condition of not

### Usage

    imbalance_score(Object, ...)

    ## S4 method for signature 'matrix'
    imbalance_score(Object, conditions, k = 10, smooth = 10)

    ## S4 method for signature 'SingleCellExperiment'
    imbalance_score(Object, dimred = 1, conditions, k = 10, smooth = 10)

### Arguments

`Object` | A `SingleCellExperiment` object or a matrix representing the reduced dimension matrix of the cells.
`...` | parameters including:
`conditions` | Either the vector of conditions, or a character indicating which column of the metadata contains this vector
`k` | The number of neighbors to consider when computing the score. Default to 10.
`smooth` | The smoothing parameter. Default to k. Lower values mean that we smooth more.
`dimred` | A string or integer scalar indicating the reduced dimension result in `reducedDims(sce)` to plot. Default to 1.

### Value

Either a list with the `scaled_scores` and the `scores` for each cell, if input is a matrix, or the `SingleCellExperiment` object, wit this list in the `colData`.

### Examples

    data("toy_dataset")
    scores <- imbalance_score(as.matrix(toy_dataset$sd[,1:2]),
      toy_dataset$sd$conditions, k = 4)
    cols <- as.numeric(cut(scores$scaled_scores, 8))
    plot(as.matrix(toy_dataset$sd[, 1:2]), xlab = "Dim1", ylab = "Dim2",
     pch = 16, col = RColorBrewer::brewer.pal(8, "Blues")[cols])

[Package condiments version 1.2.0 Index]