5 AverageHeatmap

AverageHeatmap is used to plot averaged expression cross cluster cells.

5.1 load data

httest <- system.file("extdata", "htdata.RDS", package = "scRNAtoolVis")
pbmc <- readRDS(httest)

# load markergene
markergene <- system.file("extdata", "top5pbmc.markers.csv", package = "scRNAtoolVis")
markers <- read.table(markergene, sep = ',', header = TRUE)

5.2 examples

default plot:

# plot
AverageHeatmap(object = pbmc,
               markerGene = markers$gene)

change color:

# change color
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               htCol = c("#339933", "#FFCC00", "#FF0033"))

Supporting with your own cluster colors by annoCol = TRUE and myanCol:

# change annotation color
library("scales") 
library(ggsci)

mycol <- hue_pal()(9)
mycol1 <- pal_npg()(9)

# plot
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               annoCol = TRUE,
               myanCol = mycol) +
  AverageHeatmap(object = pbmc,
                 markerGene = markers$gene,
                 annoCol = TRUE,
                 myanCol = mycol1)

Remove rownames:

# remove rownames
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               showRowNames = F)

Remove annotation name:

# remove cluster anno name
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               clusterAnnoName = F)

Mark some important genes:

# mark some genes
# tartget gene
annoGene <- c("LDHB","CCR7","LEF1","NKG7","CST7",
              "GZMK","HLA-DQA1","HLA-DRB1","HLA-DPA1")

AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               clusterAnnoName = F,
               showRowNames = F,
               markGenes = annoGene)

You can change heatmap width and height:

# change heatmap width and height
AverageHeatmap(object = pbmc,
               markerGene = markers$gene,
               clusterAnnoName = F,
               width = 8,height = 16)