iCellR (version 1.6.1)

heatmap.gg.plot: Create heatmaps for genes in clusters or conditions.

Description

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

Usage

heatmap.gg.plot(
  x = NULL,
  gene = "NULL",
  cell.sort = FALSE,
  data.type = "main",
  cluster.by = "clusters",
  conds.to.plot = NULL,
  min.scale = -2.5,
  max.scale = 2.5,
  interactive = TRUE,
  cex.col = 10,
  cex.row = 10,
  no.key = FALSE,
  out.name = "plot",
  heat.colors = c("blue", "white", "red")
)

Arguments

x

A data frame containing gene counts for cells.

gene

A set of gene names to be heatmapped.

cell.sort

If FALSE the cells will not be sorted based on their distance, default = TRUE.

data.type

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

cluster.by

Choose from "clusters" or "none", default = "clusters".

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.

cex.col

Chhose a size, default = 10.

cex.row

Choose a size, default = 10.

no.key

If you want a color legend key, default = FALSE.

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

Examples

# NOT RUN {
marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = TRUE)

MyGenes <- top.markers(marker.genes, topde = 10, min.base.mean = 0.8)

heatmap.gg.plot(demo.obj,
               gene = MyGenes,
               out.name = "plot",
               cluster.by = "clusters",
               interactive = FALSE)
# }