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############################################################
# Data
d = read.table(header = TRUE, text =
"S001 S002 S003 S004 S005 S006 S007 S008 S009 S010
Bact001 9.4 7.9 14.2 10.8 10.7 17.6 13.8 17.7 21.1 16.8
Bact002 25.3 24.4 22.9 25.6 21.2 13.6 15.2 7.7 7.3 7.5
Bact003 7.2 5.0 6.9 5.0 3.5 4.2 3.1 7.4 4.9 7.3
Bact004 21.9 23.6 17.5 18.7 25.8 24.5 22.4 15.2 30.5 22.0
Bact005 3.6 3.6 3.9 3.1 3.5 3.1 2.3 3.6 3.1 2.3
Bact006 5.6 10.1 8.9 8.7 8.9 10.9 11.3 13.5 10.1 9.3
Bact007 6.7 4.6 7.2 7.8 8.7 5.7 2.7 4.8 2.5 3.3
Bact008 3.6 2.8 3.1 3.3 3.2 3.1 3.0 3.1 2.6 2.9
Bact009 7.1 10.5 10.2 10.8 9.9 7.2 14.7 12.3 9.5 18.4
Bact010 9.7 7.6 5.1 6.1 4.6 10.1 11.6 14.6 8.2 10.2
")
d_mat = as.matrix(d)
d
############################################################
# Scaling
heatmap(d_mat, margins = c(8, 8)) # scaled for rows
heatmap(d_mat, margins = c(8, 8), scale="column")
############################################################
# Remove a Dendrogram
heatmap(d_mat, margins = c(8, 8), Colv = NA)
heatmap(d_mat, margins = c(8, 8), Rowv = NA)
############################################################
# Colors
library(RColorBrewer)
colors = colorRampPalette(c("blue", "white", "red"))(256) # Low(blue) and High(red)
heatmap(d_mat, margins = c(8, 8), col=colors)
gColors = c("orange", "skyblue")
g = factor(c(rep("Con", 5), rep("T1", 5)))
a=heatmap(d_mat, margins = c(8, 8), col=colors, Colv = NA, ColSideColors=gColors[g])
a
############################################################
# Heatmap.2
# install.packages("gplots")
library(gplots)
colors = colorRampPalette(c("blue", "white", "red"))(256) # Low(blue) and High(red)
heatmap.2(d_mat, margins = c(8, 8), dendrogram="none", scale="row", col=colors)
heatmap.2(d_mat, margins = c(8, 8), dendrogram="row", scale="row", col=colors)
heatmap.2(d_mat, margins = c(8, 8), dendrogram="row", scale="row", col=colors, trace = "none")
heatmap.2(d_mat, margins = c(8, 8), dendrogram="row", scale="row", col=colors, trace = "none", density.info = "none", Colv = NA)
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