markerExpressionPerCluster {scDataviz} | R Documentation |
Generate box-and-whisker plots illustrating marker expression per k-NN identified cluster. By default, 5 randomly-selected clusters are selected, and the expression profiles of 10 randomly-selected markers are plot across these.
markerExpressionPerCluster( indata, assay = "scaled", clusters = sample(unique(metadata(indata)[["Cluster"]]), 5), clusterAssign = metadata(indata)[["Cluster"]], markers = sample(rownames(indata), 10), ncol = 5, nrow = 2, legendPosition = "none", legendLabSize = 12, legendKeyHeight = 2.5, xlim = NULL, ylim = NULL, yfixed = FALSE, xlab = "Marker", xlabAngle = 90, xlabhjust = 0.5, xlabvjust = 0.5, ylab = "Expression", ylabAngle = 0, ylabhjust = 0.5, ylabvjust = 0.5, axisLabSize = 16, stripLabSize = 16, title = "Marker expression per cluster", subtitle = "", caption = "", titleLabSize = 16, subtitleLabSize = 12, captionLabSize = 12, borderWidth = 0.8, borderColour = "black", verbose = TRUE )
indata |
A data-frame or matrix, or SingleCellExperiment object. If a
data-frame or matrix, this should relate to expression data (cells as
columns; genes as rows). If a |
assay |
Name of the assay slot in |
clusters |
Vector containing clusters to plot. |
clusterAssign |
A vector of cell-to-cluster assignments. This can be
from any source but must align with your cells / variables. There is no
check to ensure this when |
markers |
Vector containing marker names to plot. |
ncol |
Number of columns for faceting. |
nrow |
Number of rows for faceting. |
legendPosition |
Position of legend |
legendLabSize |
Size of plot legend text. |
legendKeyHeight |
Height of the legend key. |
xlim |
Limits of the x-axis. |
ylim |
Limits of the y-axis. |
yfixed |
Logical, specifying whether or not to fix the y-axis scales across all clusters when faceting. |
xlab |
Label for x-axis. |
xlabAngle |
Rotation angle of x-axis labels. |
xlabhjust |
Horizontal adjustment of x-axis labels. |
xlabvjust |
Vertical adjustment of x-axis labels. |
ylab |
Label for y-axis. |
ylabAngle |
Rotation angle of y-axis labels. |
ylabhjust |
Horizontal adjustment of y-axis labels. |
ylabvjust |
Vertical adjustment of y-axis labels. |
axisLabSize |
Size of x- and y-axis labels. |
stripLabSize |
Size of the strip labels. |
title |
Plot title. |
subtitle |
Plot subtitle. |
caption |
Plot caption. |
titleLabSize |
Size of plot title. |
subtitleLabSize |
Size of plot subtitle. |
captionLabSize |
Size of plot caption. |
borderWidth |
Width of the border on the x and y axes. |
borderColour |
Colour of the border on the x and y axes. |
verbose |
Boolean (TRUE / FALSE) to print messages to console or not. |
Generate box-and-whisker plots illustrating marker expression per k-NN identified cluster. By default, 5 randomly-selected clusters are selected, and the expression profiles of 10 randomly-selected markers are plot across these.
A ggplot2
object.
Kevin Blighe <kevin@clinicalbioinformatics.co.uk>
# create random data that follows a negative binomial mat <- jitter(matrix( MASS::rnegbin(rexp(5000, rate=.1), theta = 4.5), ncol = 20)) colnames(mat) <- paste0('CD', 1:ncol(mat)) rownames(mat) <- paste0('cell', 1:nrow(mat)) clus <- clusKNN(mat) markerExpressionPerCluster(t(mat), clusters = c(0, 1), clusterAssign = clus)