add text on heatmap using locator()

Question

I'm creating an heatmap through heatmap.2(). I'd like to put the xaxis labels rotate of 45 degree. Following the instructions in other posts, I tried to do this building an heatmap without x labels and then using text() to add them... This is what I tried:

#fake matrix
cheese.matrix <- matrix(runif(100),10,10)
#build color palette
my.palette <- colorRampPalette(c("blue", "green", "yellow", "orange", "red"), space="rgb")
#build a first heatmap
hm_cheese <- heatmap.2(cheese.matrix,Rowv=NA,Colv=NA,col=my.palette,
                       density.info=c("none"),margins(3,5),cexRow=0.8,
                       cexCol=0.8,key=TRUE,keysize=1,trace="none",
                       lhei=c(2,8), breaks=100)
#find the coordinates on the plot where I want to pu the first and the last label
pos2 <- locator()
pos2
$x
[1] 0.08129779 0.90164993

$y
[1] -0.06905376 -0.06372554

pos2 <- structure(list(x=c(0.08129779, 0.90164993), y=c(-0.06905376, -0.06372554)), .Names=c("x","y"))
#create a vector with the labels I want to add
labs <- c("NWC1.PR", "CURD1.PR", "NWC2.PR","CURD2.PR","NWC3.PR","CURD3.PR",  "NWC4.PR", "CURD4.PR", "NWC5.PR", "CURD5.PR")
#build another heatmap
hm_cheese <- heatmap.2(cheese.matrix,Rowv=NA,Colv=NA,col=my.palette,
                      density.info=c("none"),margins(3,5),key=TRUE,
                      keysize=1,trace="none", lhei=c(2,8), breaks=100, 
                      labCol="", add.expr=text(x=seq(pos2$x[1], pos2$x[2], len=10),
                      y=rep(pos2$y[1],10), srt=45, xpd=TRUE, adj=0, labels=labs))

This put the labels on the heatmap, but all the names were overlying... I also tried this:

hm_cheese2 <-heatmap.2(cheese.matrix,Rowv=NA,Colv=NA,col=my.palette,
                       density.info=c("none"),margins(3,5),key=TRUE,keysize=1,
                       trace="none", lhei=c(2,8), breaks=100, labCol="", 
                       add.expr=text(x=seq_along(labs), y=-0.06372554, srt=45,
                       xpd=TRUE, adj=0, labels=labs))

The result was better, since the labels were along the axis, but still really close among them and overlying the plot...

Is there anything wrong in the way I used locator() to find the coordinates? Can anyone help me to improve my code?

Answer 1

You can play with argument pos in your call to text. By using pos=1 for example:

hm_cheese2 <-heatmap.2(cheese.matrix,Rowv=NA,Colv=NA,col=my.palette,
                       density.info=c("none"),margins(3,5),key=TRUE,keysize=1,
                       trace="none", lhei=c(2,8), breaks=100, labCol="", 
                       add.expr=text(x=seq_along(labs), y=-0.06372554, srt=45,
                       xpd=TRUE, adj=0, labels=labs, pos=1))

See ?text for more on pos.

If the labels fall outside the plot, you can try using xpd=NA to clip them to the device region instead of the plot or the figure regions.

hm_cheese2 <-heatmap.2(cheese.matrix,Rowv=NA,Colv=NA,col=my.palette,
                       density.info=c("none"),margins(3,5),key=TRUE,keysize=1,
                       trace="none", lhei=c(2,8), breaks=100, labCol="", 
                       add.expr=text(x=seq_along(labs), y=-0.06372554, srt=45,
                       xpd=NA, adj=0, labels=labs, pos=1))