markerExpression: Highlight the individual marker expression profile across a...
In kevinblighe/scDataviz: scDataviz: single cell dataviz and downstream analyses

Description Usage Arguments Details Value Author(s) Examples

Highlight the individual marker expression profile across a 2-dimensional reduction / embedding, typically contained within a SingleCellExperiment object. By default, this function plots the expression profile of 6 randomly-selected markers from your data.

markerExpression(
  indata,
  layout = NULL,
  assay = "scaled",
  reducedDim = "UMAP",
  dimColnames = c("UMAP1", "UMAP2"),
  markers = sample(rownames(indata), 6),
  ncol = 3,
  nrow = 2,
  col = c("darkblue", "yellow"),
  colMidpoint = 0,
  alpha = c(0, 1),
  pointSize = 0.5,
  legendPosition = "right",
  legendLabSize = 12,
  legendKeyHeight = 2.5,
  xlim = NULL,
  ylim = NULL,
  celllab = NULL,
  labSize = 3,
  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,
  stripLabSize = 16,
  title = "Individual marker expression",
  subtitle = "",
  caption = ifelse(is(indata, "SingleCellExperiment"), paste0("Total cells, ",
    nrow(as.data.frame(reducedDim(indata, reducedDim)))), paste0("Total cells, ",
    nrow(layout))),
  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 `SingleCellExperiment` object. If a data-frame or matrix, this should relate to expression data (cells as columns; genes as rows). If a `SingleCellExperiment` object, data will be extracted from an assay component named by `assay`.
`layout`	If 'indata' is a non-SingleCellExperiment object, `layout` must be activated and relate to a 2-dimensional reduction / embedding, although, technically, any data-frame or matrix of numbers will be accepted, provided that it aligns with the dimensions of `indata`, and provided that it contains columns as specified in `dimColnames`.
`assay`	Name of the assay slot in 'indata' from which data will be taken, assuming `indata` is a `SingleCellExperiment` object.
`reducedDim`	A reduced dimensional component stored within `indata`, e.g., PCA or UMAP.
`dimColnames`	The column names of the dimensions to use.
`markers`	Vector containing marker names to plot.
`ncol`	Number of columns for faceting.
`nrow`	Number of rows for faceting.
`col`	Colours used for generation of fill gradient according to expression values. Can be 2 or 3 colours.
`colMidpoint`	Mid-point (expression value) for the colour range. Only used when 3 colours are specified by `col`.
`alpha`	Control the gradient of colour transparency, with 1 being opaque.
`pointSize`	Size of plotted points.
`legendPosition`	Position of legend `('top', 'bottom', 'left', 'right', 'none')`.
`legendLabSize`	Size of plot legend text.
`legendKeyHeight`	Height of the legend key.
`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.
`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.
`stripLabSize`	Size of the strip (marker) 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 `('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash')`.
`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 `('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash')`.
`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.

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)

markerExpression(t(mat), layout = u)