Dear R Community,
I am trying to create an heatmap for the following set of data:
##example of data matrix
o4
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18
green 27 28 29 29 28 28 26 25 25 23 23 22 22 21 21 22 22 22
yellow 6 8 8 7 7 7 6 6 6 7 7 7 6 6 6 6 6 5
red 15 15 15 15 15 15 14 13 12 11 12 10 9 8 7 6 8 9
pink 11 11 11 11 11 10 12 11 13 14 14 15 15 14 14 17 17 17
blue 17 15 15 16 17 17 17 17 18 18 18 19 20 20 20 21 22 21
the column names are timepoints 450 in total. When I run the heatmap code:
x <- as.matrix(o4)
ramp <- colorRamp(c("yellow","green","blue"))
cv<-rgb( ramp(seq(0, 1, length = 83)), max = 255)
heatmap(x, col = cv, Colv=NA, Rowv=NA,xaxt="n", yaxt="n",
scale="column", margins=c(5,10), labCol=NA,xlab = "Time", ylab= "Colors",
main = "")
I have quite few problems to change the column names. Being 450
timepoints too many to be readable on the plot, I wanted to
reduce/scale them to, let say 45. So, as you can see from the code
above, I have removed the x and y, row and column information.
Then I have tried to create a new name vector:
##create col vector to add names
Colname<-as.character(seq(0,4500,500))
##putting it as arguments of (labCol=Colname, in the heatmap function)
but this solution didn't work. It looks like as it cannot find the
exact point on the axis where to stick the label in and it clutters
all the datapoint on the same spot without being able to unfold it.
Therefore I have tried to introduce an axis:
axis(1, at=seq(0,450,1),line=1)
and then adding some text on top
mtext(paste(seq(0,4500, 250),sep=""),side=1,
at=seq(0,450,25),line=2,cex=0.6,las=1)
also this way didn't work out. Actually, it has created a kind of axis
but the zero of it was aligned to the middle of the plot. So, it was
completely shifted.
That was my first problem.
Second small problem.
I am trying to mark on the heatmap some crucial timepoints. I wanted
to do it by adding a straight abline on the heatmap plot
abline(v=80,col=green)
but also this doesn't seem to have any result
It seems that it is quite difficult to add any information to the
heatmap, but perhaps some of you might know how to do it.
Many thanks in advance
Moreno
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