florets: Draw coxcomb plots as points in a graphics window

In Nanostring-Biostats/SpatialDecon: Deconvolution of mixed cells from spatial and/or bulk gene expression data

Draw coxcomb plots as points in a graphics window

Description

Draws a scatterplot where each point is a circular barplot, intended to show decon results

Usage

florets(
  x,
  y,
  b,
  col = NULL,
  legendwindow = FALSE,
  rescale.by.sqrt = TRUE,
  border = NA,
  add = FALSE,
  cex = 1,
  bty = "n",
  xaxt = "n",
  yaxt = "n",
  xlab = "",
  ylab = "",
  ...
)

Arguments

x	Vector of x coordinates
y	Vector of y coordinates
b	matrix or cell abundances, with columns aligned with the elements of x and y
col	vector of colors, aligned to the rows of b.
legendwindow	Logical. If TRUE, the function draws a color legend in a new window
rescale.by.sqrt	Logical, for whether to rescale b by its square root to make value proportional to shape area, not shape length.
border	Color of pie segment border, defauls to NA/none
add	Logical. If TRUE, the function draws florets atop an existing graphics device (TRUE) or call a new device (FALSE).
cex	Floret size. Florets are scaled relative to the range of x and y; this further scales up or down.
bty	bty argument passed to plot()
xaxt	xaxt argument passed to plot()
yaxt	yaxt argument passed to plot()
xlab	xlab, defaults to ""
ylab	ylab, defaults to ""
...	additional arguments passed to plot()

Value

Draws a coxcomb plot, returns no data.

Examples

data(mini_geomx_dataset)
data(safeTME)
# estimate background:
mini_geomx_dataset$bg <- derive_GeoMx_background(
  norm = mini_geomx_dataset$normalized,
  probepool = rep(1, nrow(mini_geomx_dataset$normalized)),
  negnames = "NegProbe"
)
# run basic decon:
res0 <- spatialdecon(
  norm = mini_geomx_dataset$normalized,
  bg = mini_geomx_dataset$bg,
  X = safeTME
)
# draw florets:
florets(
  x = mini_geomx_dataset$annot$x,
  y = mini_geomx_dataset$annot$y,
  b = res0$beta, cex = 2
)

Nanostring-Biostats/SpatialDecon documentation built on Jan. 26, 2024, 8:20 p.m.