plotDecontXMarkerExpression {celda} | R Documentation

## Plots expression of marker genes before and after decontamination

### Description

Generates a violin plot that shows the counts of marker genes in cells across specific clusters or cell types. Can be used to view the expression of marker genes in different cell types before and after decontamination with `decontX`.

### Usage

    plotDecontXMarkerExpression(
      x,
      markers,
      groupClusters = NULL,
      assayName = c("counts", "decontXcounts"),
      z = NULL,
      exactMatch = TRUE,
      by = "rownames",
      log1p = FALSE,
      ncol = NULL,
      plotDots = FALSE,
      dotSize = 0.1
    )

### Arguments

`x` | Either a SingleCellExperiment or a matrix-like object of counts.
`markers` | Character Vector or List. A character vector or list of character vectors with the names of the marker genes of interest.
`groupClusters` | List. A named list that allows cell clusters labels coded in `z` to be regrouped and renamed on the fly. For example, `list(Tcells=c(1, 2), Bcells=7)` would recode clusters 1 and 2 to "Tcells" and cluster 7 to "Bcells". Note that if this is used, clusters in `z` not found in `groupClusters` will be excluded. Default `NULL`.
`assayName` | Character vector. Name(s) of the assay(s) to plot if `x` is a SingleCellExperiment. If more than one assay is listed, then side-by-side violin plots will be generated. Default `c("counts", "decontXcounts")`.
`z` | Character, Integer, or Vector. Indicates the cluster labels for each cell. If `x` is a SingleCellExperiment and `z = NULL`, then the cluster labels from `decontX` will be retreived from the `colData` of `x` (i.e. `colData(x)$decontX_clusters`). If `z` is a single character or integer, then that column will be retrived from `colData` of `x`. (i.e. `colData(x)[,z]`). If `x` is a counts matrix, then `z` will need to be a vector the same length as the number of columns in `x` that indicate the cluster to which each cell belongs. Default `NULL`.
`exactMatch` | Boolean. Whether to only identify exact matches for the markers or to identify partial matches using `grep`. See `retrieveFeatureIndex` for more details. Default `TRUE`.
`by` | Character. Where to search for the markers if `x` is a SingleCellExperiment. See `retrieveFeatureIndex` for more details. If `x` is a matrix, then this must be set to `"rownames"`. Default `"rownames"`.
`log1p` | Boolean. Whether to apply the function `log1p` to the data before plotting. This function will add a pseudocount of 1 and then log transform the expression values. Default `FALSE`.
`ncol` | Integer. Number of columns to make in the plot. Default `NULL`.
`plotDots` | Boolean. If `TRUE`, the expression of features will be plotted as points in addition to the violin curve. Default `FALSE`.
`dotSize` | Numeric. Size of points if `plotDots = TRUE`. Default `0.1`.

### Value

Returns a `ggplot` object.

### Author(s)

Shiyi Yang, Joshua Campbell

### See Also

See `decontX` for a full example of how to estimate and plot contamination.

[Package celda version 1.8.1 Index]