bubble.gg.plot {iCellR}

Create bubble heatmaps for genes in clusters or conditions.

Description

This function takes an object of class iCellR and genes and provides a heatmap.

Usage

bubble.gg.plot(
  x = NULL,
  gene = "NULL",
  data.type = "main",
  conds.to.plot = NULL,
  min.scale = -2.5,
  max.scale = 2.5,
  interactive = TRUE,
  colour = "Expression",
  size = "Percent.Expressed",
  out.name = "plot",
  heat.colors = c("blue", "red")
)

Arguments

x

A data frame containing gene counts for cells.

gene

A set of gene names to be heatmapped.

data.type

Choose from "main", "atac", atac.imputed and "imputed", default = "main".

conds.to.plot

Choose the conditions you want to see in the plot, default = NULL (all conditions).

min.scale

Set a minimum color scale, default = -2.5.

max.scale

Set a maximum color scale, default = 2.5.

interactive

If TRUE an html interactive file will be made, default = TRUE.

colour

Set color to "Percent.Expressed", or "Expression", , default = "Expression".

size

Set size to "Percent.Expressed", or "Expression", , default = "Percent.Expressed".

out.name

Output name for html file if interactive = TRUE, default = "plot".

heat.colors

Colors for heatmap, default = c("blue" ,"white", "red").

Value

An object of class iCellR