[BioC] Generating heat map of pre-organised data in matrix without clustering using ggplot2 or heatmap.2

[Jakub Stanislaw Nowak]

Hello bioconductor friends,

I am trying to generate heatmaps for my data and run in following problems. I would be grateful for some suggestions about heat map code. 

I arranged matrix for the heatmap by myself and I would like to keep this not changed during heat map plotting. I tried both heatmap.2 (gplot) and geom_tile (ggplot2)

1. So when I used heatmap.2 from (gpot) it keeps my matrix sort but I have problems making the layout look nice. Below is the code I used.
Can you suggest how to:
a) make rows and columns separated and rows bigger so it can read easier.
b) is there a way for changing  x label for key so it includes min and max values for colour code.
c) can the density plot be generated above the key

Preparing table for the heatmap.2 from (qplot)
---------------------------------------
```{r}
data.heatmap <- data.sorted.merged[,-c(2:5,8),drop=FALSE]
rownames(data.heatmap)<-data.heatmap$ID
data.heatmap <- data.heatmap[,-1]
data.heatmap.matrix <- data.matrix(data.heatmap)
```
Generating heatmap with heatmap.2
------------------------------
```{r}
if (!require("gplots")) {
 install.packages("gplots", dependencies = TRUE)
 library(gplots)
 }
if (!require("RColorBrewer")) {
 install.packages("RColorBrewer", dependencies = TRUE)
 library(RColorBrewer)
 }
mypalette <- colorRampPalette(c("red", "yellow", "green"))(n = 299)
#subseting default gradient with custom one for better visualisation
colbreaks <- c(seq(-6,-3,length=110), # for red
seq(-3,3,length=90), # for yellow
seq(3.10,length=100)) # for green
heatmap.2(data.heatmap.matrix,
  main = "Correlation", # heat map title
  notecol="black",      # change font color of cell labels to black
  density.info="density",  # turns density plot inside color legend
  trace="none",# turns off trace lines inside the heat map
  scale=c("none"),
  colsep, rowsep, sepcolor="white", sepwidth=c(1,1), #doesn't really show any separation
  margins =c(1,15),     # widens margins around plot doesn't do much 
  col=mypalette,       # use on color palette defined earlier 
  breaks=colbreaks,    # enable color transition at specified limits
  Rowv="NA",     # only draw a row dendrogram
  Colv="NA",    # turn off column clustering
  key.title=NA, # no title
  symkey=FALSE,
  
  )
```

2. I also tried to use geom_tile from (ggplot2) to generate this heat map. Here layout looks better but I am loosing my organisation of the matrix. Below is a code I used to make a plot
Can you suggest:
1. how to switch off clustering in ggplot2

Generating heatmap with ggplot2 

```{r}
if (!require("reshape2")) {
 install.packages("reshape2", dependencies = TRUE)
 library(reshape2)
 }
if (!require("plyr")) {
 install.packages("plyr", dependencies = TRUE)
 library(plyr)
 }
if (!require("scales")) {
 install.packages("scales", dependencies = TRUE)
 library(scales)
 }
if (!require("ggplot2")) {
 install.packages("ggplot2", dependencies = TRUE)
 library(ggplot2)
 }
data.sorted.merged.test <- data.sorted.merged[,-c(2:5,8)]
data.heatmap2 <- melt(data.sorted.merged.test)
data.heatmap2 <- ddply(data.heatmap2, .(variable), transform,rescale = rescale(value))
ggplot(data.heatmap2, aes(variable, ID))+ geom_tile(aes(fill=rescale), colour="white") + 
  scale_fill_gradient(low="white", high="red", breaks=colbreaks)
```

Also I can attach png files of the heat map if that can help.

Thanks very much for your help,

Jakub


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