plotClusters: Highlight cell-to-cluster assignments across a 2-dimensional...

Description Usage Arguments Details Value Author(s) Examples

View source: R/plotClusters.R

Description

Highlight cell-to-cluster assignments across a 2-dimensional reduction / embedding.

Usage

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plotClusters(
  indata,
  clusterVector = NULL,
  reducedDim = "UMAP",
  dimColnames = c("UMAP1", "UMAP2"),
  clusterColname = "Cluster",
  pointSize = 0.5,
  legendPosition = "none",
  legendLabSize = 12,
  xlim = NULL,
  ylim = NULL,
  label = TRUE,
  labSize = 5,
  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 = "k-nearest neighbour (k-NN) clusters",
  subtitle = "",
  caption = ifelse(is(indata, "SingleCellExperiment"), paste0("Total cells, ",
    nrow(as.data.frame(reducedDim(indata, reducedDim)))), paste0("Total cells, ",
    length(clusterVector))),
  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",
  verbose = TRUE
)

Arguments

indata

A data-frame or matrix, or SingleCellExperiment object. If a data-frame or matrix, columns named in dimColnames will be extracted from the data and used to generate the plot. If a SingleCellExperiment object, a reduction named by reducedDim will be taken from your object and used to generate the plot, again using columns whose names are specified in dimColnames.

clusterVector

If indata is a non-SingleCellExperiment object, clusterVector must be non-NULL and relate to a cell-to-cluster assignment whose length matches nrow(indata).

reducedDim

A reduced dimensional embedding stored within 'indata', e.g., PCA or UMAP.

dimColnames

The column names of the dimensions to use.

clusterColname

The column name in the metadata of indata that contains the cell-to-cluster assignment, assuming indata is a SingleCellExperiment object.

pointSize

Size of plotted points.

legendPosition

Position of legend ('top', 'bottom', 'left', 'right', 'none').

legendLabSize

Size of plot legend text.

xlim

Limits of the x-axis.

ylim

Limits of the y-axis.

label

Logical, indicating whether or not to label the clusters.

labSize

Size of labels.

drawConnectors

Logical, indicating whether or not to connect plot labels to their corresponding cluster islands 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 ('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.

verbose

Boolean (TRUE / FALSE) to print messages to console or not.

Details

Highlight cell-to-cluster assignments across a 2-dimensional reduction / embedding.

Value

A ggplot2 object.

Author(s)

Kevin Blighe <kevin@clinicalbioinformatics.co.uk>

Examples

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# 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)
clusvec <- clusKNN(u$layout)
plotClusters(u$layout, clusvec)

kevinblighe/scToolkit documentation built on Sept. 25, 2021, 11:29 p.m.