spatial.plot: Plot nGenes, UMIs and perecent mito, genes, clusters and more on spatial image

Description

This function takes an object of class iCellR and creates spatial plots.

Usage

spatial.plot(
  x = NULL,
  cell.size = 1,
  cell.colors = c("gray", "red"),
  back.col = "black",
  col.by = "clusters",
  conds.to.plot = NULL,
  gene = NULL,
  data.type = "main",
  scaleValue = TRUE,
  min.scale = 0,
  max.scale = 2.5,
  anno.clust = FALSE,
  anno.size = 4,
  anno.col = "white",
  cell.transparency = 1,
  interactive = TRUE,
  out.name = "plot"
)

Value

An object of class iCellR.

Arguments

x: An object of class iCellR.
cell.size: A numeric value for the size of the cells, default = 1.
cell.colors: Colors for heat mapping the points in "scatterplot", default = c("gray","red").
back.col: A color for the plot background, default = "black".
col.by: Choose between "clusters", "mt","UMIs","nGenes", "cc" (cell cycle) or "gene", default = "clusters".
conds.to.plot: Choose the conditions you want to see in the plot, default = NULL (all conditions).
gene: Gene name/names to be plotted, if col.by = "gene".
data.type: Choose from "main" or "imputed", default = "main".
scaleValue: Scale the colors, default = FALSE.
min.scale: If scaleValue = TRUE, set a number for min, default = -2.5.
max.scale: If scaleValue = TRUE, set a number for max, default = 2.5.
anno.clust: Annotate cluster names on the plot, default = TRUE.
anno.size: If anno.clust is TRUE set font size, default = 3.
anno.col: If anno.clust is TRUE set color, default = "white".
cell.transparency: Color transparency for points in "scatterplot" and "boxplot", default = 1.
interactive: If set to TRUE an interactive HTML file will be created, default = TRUE.
out.name: If "interactive" is set to TRUE, the out put name for HTML, default = "plot".