# ============================================================
# Tutorial on drawing a heatmap using ggplot2
# by Umer Zeeshan Ijaz (http://userweb.eng.gla.ac.uk/umer.ijaz)
# =============================================================
abund_table<-read.csv("SPE_pitlatrine.csv",row.names=1,check.names=FALSE)
# Transpose the data to have sample names on rows
abund_table<-t(abund_table)
# Convert to relative frequencies
abund_table <- abund_table/rowSums(abund_table)
library(reshape2)
df<-melt(abund_table)
colnames(df)<-c("Samples","Species","Value")
library(plyr)
library(scales)

# We are going to apply transformation to our data to make it
# easier on eyes 

#df<-ddply(df,.(Samples),transform,rescale=scale(Value))
df<-ddply(df,.(Samples),transform,rescale=sqrt(Value))

# Plot heatmap
p <- ggplot(df, aes(Species, Samples)) + 
  geom_tile(aes(fill = rescale),colour = "white") + 
  scale_fill_gradient(low = "white",high = "steelblue")+
  scale_x_discrete(expand = c(0, 0)) +
  scale_y_discrete(expand = c(0, 0)) + theme(legend.position = "none",axis.ticks = element_blank(),axis.text.x = element_text(angle = 90, hjust = 1,size=5),axis.text.y = element_text(size=5))

pdf("Heatmap.pdf")
print(p)
dev.off()