tessViz: Plot tesselated object.

In ludvigla/spaceST: spaceST

Description

Sisualize some value on an ST grid using voronoi tesselation.

Usage

tessViz(object, select.columns = 1:3, xlim = c(0, 34), ylim = c(0,
  36), scale.by.column = FALSE, datatype = "topics", add.points = F,
  outline.color = NA, bg = "black", inv.col = F, alpha = 1,
  scatter = NULL, return.list = FALSE, cell.col = "cyan",
  cell.size = 0.01, cell.alpha = 0.1, palette = "offwhite.to.black",
  max.num.cols = 20, polygon.mask = TRUE, fill.empty = FALSE, ...)

Arguments

object	Sbject of class spaceST.
select.columns	Select columns of target matrix [default = 1:3].
xlim	Set limits of x axis [default = c(0, 36)].
ylim	Set limits of y axis [default = c(0, 36)].
scale.by.column	Should columns be scaled independently? [default = FALSE].
datatype	Select target matrix from spaceST object [default = "topics"].
add.points	Should points be added to the plot?
outline.color	Set polygon outline color [default = NA].
bg	Select background color [default = "black"].
inv.col	Invert colors [default = FALSE].
alpha	Set alpha of polygons [default = 1].
scatter	Provide list of data.frames with coordinates to overlay tesselated surface. Colnames have to be c("x", "y") [default = NULL].
return.list	Return list of plots instead of combining them into a grid [default = FALSE].
cell.col	Color of points (spots or scatter) [default = "cyan"].
cell.size	Size of points (spots or scatter) [default = 0.01].
cell.alpha	Color of points (spots or scatter) [default = 0.1].
palette	Select color palette palette.select.
max.num.cols	Select maximum number of columns to plot [default = 20].
polygon.mask	Logical; Specify whether or not the background should be masked [default = TRUE].
fill.empty	Fill empty array spots with 0 values.
...	Parameters passed to geom_point().

ludvigla/spaceST documentation built on May 29, 2019, 3:43 a.m.