Introduction to Biostatistical Computing PHC 6937
R graphics heatmap.2
Zhiguang Huo (Caleb)
Monday September 19, 2022
Heatmap.2
library(gplots) ## heatmap.2 is available in gplots
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess
Application on Iris data
dataMatrix <- as.matrix(iris[,1:4])
heatmap.2(dataMatrix)
dataMatrix <- as.matrix(iris[,1:4])
heatmap.2(dataMatrix, trace = "none")
dataMatrix2 <- as.matrix(iris[1:5,1:4])
heatmap.2(dataMatrix2, trace = "none",
cellnote = dataMatrix2, notecol = "black")
dataMatrix <- as.matrix(iris[,1:4])
species <- iris$Species
color0 <- species
levels(color0) <- palette()[1:length(levels(species))]
color <- as.character(color0)
heatmap.2(dataMatrix, trace = "none", RowSideColors = color)
legend("topright", legend=levels(species),fill=levels(color0))
- Remove automatical reordering of rows and columns
dataMatrix <- as.matrix(iris[,1:4])
species <- iris$Species
color0 <- species
levels(color0) <- palette()[1:length(levels(species))]
color <- as.character(color0)
heatmap.2(dataMatrix, trace = "none", RowSideColors = color,
Colv=NA, Rowv = NA )
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column
## dendogram.
legend("topright", legend=levels(species),fill=levels(color0))
- Standardize each row to mean 0 and sd 1
dataMatrix <- as.matrix(iris[,1:4])
species <- iris$Species
color0 <- species
levels(color0) <- palette()[1:length(levels(species))]
color <- as.character(color0)
heatmap.2(dataMatrix, trace = "none", RowSideColors = color,
Colv=NA, Rowv = NA , scale = "row")
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column
## dendogram.
legend("topright", legend=levels(species),fill=levels(color0))
- Try other colors
- heat.colors (default)
- redgreen
- greenred
- grey.colors
- bluered
- cm.colors
- rainbow
- terrain.colors
- topo.colors
dataMatrix <- as.matrix(iris[,1:4])
species <- iris$Species
color0 <- species
levels(color0) <- palette()[1:length(levels(species))]
color <- as.character(color0)
heatmap.2(dataMatrix, trace = "none",
RowSideColors = color, col = bluered,
Colv=NA, Rowv = NA , scale = "row")
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column
## dendogram.
legend("topright", legend=levels(species),fill=levels(color0))
Adjust legend positions
dataMatrix <- as.matrix(iris[,1:4])
species <- iris$Species
color0 <- species
levels(color0) <- palette()[1:length(levels(species))]
color <- as.character(color0)
heatmap.2(dataMatrix, trace = "none",
RowSideColors = color, col = bluered,
Colv=NA, Rowv = NA , scale = "row",
margins = c(6,6))
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
## Warning in heatmap.2(dataMatrix, trace = "none", RowSideColors = color, :
## Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column
## dendogram.
par(xpd=TRUE) ## default is FALSE, allow legend outside the plotting area
legend(x = 0.7, y = 1.1, legend=levels(species),fill=levels(color0))
