Plots expression of marker genes before and after decontamination

Source: R/plot_decontx.R

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.

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.

See also

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

Author

Shiyi Yang, Joshua Campbell