Plots percentage of cells cell types expressing markers

Generates a barplot that shows the percentage of cells within clusters or cell types that have detectable levels of given marker genes. Can be used to view the expression of marker genes in different cell types before and after decontamination with decontX.

plotDecontXMarkerPercentage(
  x,
  markers,
  groupClusters = NULL,
  assayName = c("counts", "decontXcounts"),
  z = NULL,
  threshold = 1,
  exactMatch = TRUE,
  by = "rownames",
  ncol = round(sqrt(length(markers))),
  labelBars = TRUE,
  labelSize = 3
)

Arguments

x

Either a SingleCellExperiment or a matrix-like object of counts.

markers

List. A named list indicating the marker genes for each cell type of interest. Multiple markers can be supplied for each cell type. For example, list(Tcell_Markers=c("CD3E", "CD3D"), Bcell_Markers=c("CD79A", "CD79B", "MS4A1") would specify markers for human T-cells and B-cells. A cell will be considered "positive" for a cell type if it has a count greater than threshold for at least one of the marker genes in the list.

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 from the barplot. 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 barplots 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 retived 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.

threshold

Numeric. Markers greater than or equal to this value will be considered detected in a cell. Default 1.

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".

ncol

Integer. Number of columns to make in the plot. Default round(sqrt(length(markers)).

labelBars

Boolean. Whether to display percentages above each bar Default TRUE.

labelSize

Numeric. Size of the percentage labels in the barplot. Default 3.

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