spatial.plot: Plot nGenes, UMIs and perecent mito, genes, clusters and more...
In rezakj/iCellR: Analyzing High-Throughput Single Cell Sequencing Data

spatial.plot

R Documentation

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"
)

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".