metadataPlot {scDataviz} | R Documentation |
SingleCellExperiment
object.Colour shade a 2-dimensional reduction / embedding based on metadata, typically contained within a SingleCellExperiment
object.
metadataPlot( indata, meta = NULL, reducedDim = "UMAP", dimColnames = c("UMAP1", "UMAP2"), colby = NULL, colkey = NULL, pointSize = 0.5, legendPosition = "right", legendLabSize = 12, legendIconSize = 5, xlim = NULL, ylim = NULL, celllab = NULL, labSize = 3, labhjust = 1.5, labvjust = 0, drawConnectors = TRUE, widthConnectors = 0.5, colConnectors = "black", xlab = dimColnames[1], xlabAngle = 0, xlabhjust = 0.5, xlabvjust = 0.5, ylab = dimColnames[2], ylabAngle = 0, ylabhjust = 0.5, ylabvjust = 0.5, axisLabSize = 16, title = "Metadata plot", subtitle = "", caption = ifelse(is(indata, "SingleCellExperiment"), paste0("Total cells, ", nrow(as.data.frame(reducedDim(indata, reducedDim)))), paste0("Total cells, ", nrow(meta))), titleLabSize = 16, subtitleLabSize = 12, captionLabSize = 12, hline = NULL, hlineType = "longdash", hlineCol = "black", hlineWidth = 0.4, vline = NULL, vlineType = "longdash", vlineCol = "black", vlineWidth = 0.4, gridlines.major = TRUE, gridlines.minor = TRUE, borderWidth = 0.8, borderColour = "black" )
indata |
A data-frame or matrix, or |
meta |
If 'indata' is a non-SingleCellExperiment object, 'meta' must be
activated and relate to a data-frame of metadata that aligns with the rows
of |
reducedDim |
A reduced dimensional embedding stored within |
dimColnames |
The column names of the dimensions to use. |
colby |
If NULL, all points will be coloured differently. If not NULL,
the value is assumed to be a column name in |
colkey |
Vector of name-value pairs relating to value passed to 'col',
e.g., |
pointSize |
Size of plotted points. |
legendPosition |
Position of legend |
legendLabSize |
Size of plot legend text. |
legendIconSize |
Size of plot legend icons / symbols. |
xlim |
Limits of the x-axis. |
ylim |
Limits of the y-axis. |
celllab |
A vector containing any cells that the user wishes to label in the plot. |
labSize |
Size of labels. |
labhjust |
Horizontal adjustment of label. |
labvjust |
Vertical adjustment of label. |
drawConnectors |
Logical, indicating whether or not to connect plot labels to their corresponding points by line connectors. |
widthConnectors |
Line width of connectors. |
colConnectors |
Line colour of connectors. |
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. |
title |
Plot title. |
subtitle |
Plot subtitle. |
caption |
Plot caption. |
titleLabSize |
Size of plot title. |
subtitleLabSize |
Size of plot subtitle. |
captionLabSize |
Size of plot caption. |
hline |
Draw one or more horizontal lines passing through this/these values on y-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90). |
hlineType |
Line type for hline |
hlineCol |
Colour of hline. |
hlineWidth |
Width of hline. |
vline |
Draw one or more vertical lines passing through this/these values on x-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90). |
vlineType |
Line type for vline |
vlineCol |
Colour of vline. |
vlineWidth |
Width of vline. |
gridlines.major |
Logical, indicating whether or not to draw major gridlines. |
gridlines.minor |
Logical, indicating whether or not to draw minor gridlines. |
borderWidth |
Width of the border on the x and y axes. |
borderColour |
Colour of the border on the x and y axes. |
Colour shade a 2-dimensional reduction / embedding based on metadata, typically contained within a SingleCellExperiment
object.
A ggplot2
object.
Kevin Blighe <kevin@clinicalbioinformatics.co.uk>
# create random data that follows a negative binomial mat <- jitter(matrix( MASS::rnegbin(rexp(1000, rate=.1), theta = 4.5), ncol = 20)) colnames(mat) <- paste0('CD', 1:ncol(mat)) rownames(mat) <- paste0('cell', 1:nrow(mat)) u <- umap::umap(mat)$layout colnames(u) <- c('UMAP1','UMAP2') rownames(u) <- rownames(mat) metadata <- data.frame( group = c(rep('PB1', 25), rep('PB2', 25)), row.names = rownames(u)) metadataPlot(u, meta = metadata, colby = 'group')