heatmaps: Visualize spatial heatmaps
In ludvigla/spaceST: spaceST

Generates a scatter plot of array spots colored by some value.

spatial.heatmap(object, value, type = "expr", HE.list = NULL,
  palette = "spectral", invert.heatmap = FALSE, hide.legend = FALSE,
  bg.black = FALSE, xlim = c(1, 33), ylim = c(1, 35), ncols = NULL,
  arrange = TRUE, col.title = NULL, scale = "", size = 3,
  hide.dropouts = F, ...)

`object`	Object of class spaceST.
`value`	Target vector to visualize. This value can be chosen from any slot of the spaceST object containing data linked to array spots.
`type`	Select dataset where the value can be found [options: "expr", "norm.data", "pca"]
`HE.list`	List of paths to HE images in jpeg format that should be used as a background for the spatial heatmap.
`palette`	Color palette used for spatial heamtap [options: ""expr", "green.to.blue", "spectral", "offwhite.to.black", " "viridis", "magma", "plasma", "cividis"]
`invert.heatmap`	Invert color gradient.
`hide.legend`	Exclude legend.
`bg.black`	Set background color to black.
`xlim, ylim`	Set limits of x/y axes. [default: xlim = c(1, 34), ylim = c(1, 36)]
`ncols`	Number of columns in arranged plot table.
`arrange`	Arrange plots.
`col.title`	Give the color legend a title.
`scale`	Set this parameter to "colwise" to scale each column separately.
`size`	Set size of markers.
`hide.dropouts`	Logical; Set to TRUE if you want to hide spots with 0 values.
`...`	Parameters passed to geom_point.