Hi folks, I have been working with the ellipse library and trying to use the heatmap.2 function. I have called the function as follows hh <- heatmap.2(DATA, Rowv= F, trace = "none", colsep=seq(1, 4), rowsep = seq(1,dim(GENES)[1]), col = brewer.pal(9, "YlOrRd"), lmat=rbind( c(3, 4,0), c(2,1,1)), lwid=c(0.2, 1,0.5 ), lhei= c (0.18,0.5), breaks = br1) where DATA is a numeric matrix and>br1[1] 0.0000000 0.5337751 1.0675502 1.6013253 2.1351003 2.6688754 3.2026505 3.7364256 4.2702007 [10] 4.8039758 when I try to change the breaks by using br2, which is> br2[1] 0.0000000 0.5337751 1.0675502 1.6013253 2.1351003 3.0000000 3.5000000 4.0000000 4.5000000 [10] 4.8039758 I get the correct heatmap representation but the color key does not correctly update to reflect the changes in breaks even though the superimposed histogram is also corrected. I looked at the souce code for heatmap.2. The relevant section of the function that outputs the color key begins at line 324. Any suggestions to fix this problem? Thanks for any help on this! John Celniker
Hi folks,
I have been working with the ellipse library and trying to use the
heatmap.2 function. I have called the function as follows
hh <- heatmap.2(DATA, Rowv= F, trace = "none",
colsep=seq(1, 4), rowsep = seq(1,dim(GENES)[1]), col brewer.pal(9,
"YlOrRd"),
lmat=rbind( c(3, 4,0), c(2,1,1)), lwid=c(0.2, 1,0.5 ), lhei= c
(0.18,0.5),
breaks = br1)
where DATA is a numeric matrix and>br1
[1] 0.0000000 0.5337751 1.0675502 1.6013253 2.1351003 2.6688754
3.2026505 3.7364256 4.2702007
[10] 4.8039758
when I try to change the breaks by using br2, which is> br2
[1] 0.0000000 0.5337751 1.0675502 1.6013253 2.1351003 3.0000000
3.5000000 4.0000000 4.5000000
[10] 4.8039758
I get the correct heatmap representation but the color key does not
correctly update to reflect the changes in breaks even though the
superimposed histogram is also corrected.
I looked at the souce code for heatmap.2. The relevant section of the
function that outputs the color key begins at line 324. Any
suggestions to fix this problem?
Thanks for any help on this!
John Celniker
Hi folks,
I have been working with the ellipse library and trying to use the
heatmap.2 function. I have called the function as follows
hh <- heatmap.2(DATA, Rowv= F, trace = "none",
colsep=seq(1, 4), rowsep = seq(1,dim(GENES)[1]), col brewer.pal(9,
"YlOrRd"),
lmat=rbind( c(3, 4,0), c(2,1,1)), lwid=c(0.2, 1,0.5 ), lhei= c
(0.18,0.5),
breaks = br1)
where DATA is a numeric matrix and>br1
[1] 0.0000000 0.5337751 1.0675502 1.6013253 2.1351003 2.6688754
3.2026505 3.7364256 4.2702007
[10] 4.8039758
when I try to change the breaks to:> br2
[1] 0.0000000 0.5337751 1.0675502 1.6013253 2.1351003 3.0000000
3.5000000 4.0000000 4.5000000
[10] 4.8039758
I get the correct heatmap representation but the color key does not
update correctly to reflect changes in breaks even though the
superimposed histogram is correct.
I looked at the souce code for heatmap.2. The relevant section of the
function that outputs the color key begins at line 324, but I could
not figure out how I could fix it.
Thanks for any help on this!
John Celniker