dotPlot: Plots matrix as dotPlot

In iaaka/visutils: QC, analyse and visualize visium

Plots matrix as dotPlot

Description

Shows values in matix by point size and color. Size matrix (m) is not scaled by default, dot size is defined as m*max.cex

Usage

dotPlot(
  m,
  mc = m,
  rfun = sqrt,
  colfun = function(x) num2col(x, c("white", "yellow", "violet", "black")),
  grid = TRUE,
  grid.lty = 2,
  grid.col = "gray",
  max.cex = 1,
  xlab = "",
  ylab = "",
  ylab.cex = 1,
  xlab.cex = 1,
  colColours = NULL,
  rowColours = NULL,
  rowAnnWidth = 1,
  colAnnWidth = 1,
  scaleWM = FALSE,
  pch = 19,
  plot.legend = TRUE,
  legend.cex.at = NULL,
  legend.col.at = legend.cex.at,
  legend.cex.title = "",
  legend.col.title = "",
  ...
)

Arguments

m	numeric matrix to be shown as dot size
mc	numeric matrix to be shown as dot colour (uses m as default)
rfun	function to calculate radius from matrix values. Use sqrt (default) to make area proportional to value
colfun	function to transform values to colour gradient
grid	logial, should grid be plotted
grid.lty	lty of grid
grid.col	line color of grid
max.cex	max size of dots
xlab, ylab	axis labels
ylab.cex	magnification label for ylabs
colColours	colour matrix to plot annotation for columns (matrix with nrow equal to ncol(m); each column of colColours is annotation)
rowColours	colour matrix to plot annotation for row (matrix with nrow equal to nrow(m); each column of rowColours is annotation)
rowAnnWidth, colAnnWidth	size of colour annotations in user coordinates
scaleWM	logical, specifies wheter computed radiuses should be scaled into 0,1 interval (FALSE by default).
pch	point character (19 by default)
plot.legend	logical, whether legend should be plotted. Single legend will be plotted if m is identicall to mc.
legend.cex.at, legend.col.at	values to be used in legend, set both to have two independent legends for size and colour
legend.cex.title, legend.col.title	titles of legends
...	other parameters to be passed to plot function

Examples

c = matrix(1:12,ncol=3)
par(mar=c(4,4,1,10),bty='n')
dotPlot(c/12,-c,max.cex = 3,colColours = cbind(col1=c('red','blue','red'),col2=c('green','green','magenta')),
        rowColours = cbind(rrr1=c('red','blue','blue','red'),rrr2=c('green','green','magenta','green')),
      legend.cex.title='size',legend.col.title='col',
      colAnnWidth = 0.5,
      rowAnnWidth = 0.5)

iaaka/visutils documentation built on Jan. 17, 2025, 11:29 p.m.