Hi,
I'm using the latticeExtra package's dendrogramGrob function to create a
grob with both a dendrogram and a covariate bar (via the 'add'
parameter). When the dendrogram has very short branches at its leaves, it
appears as a line and becomes impossible to see when placed next to the
covariate bar.
For example:> x <- outer(-5:5, -5:5, "*") + matrix(nrow = 11, ncol = 11,
data = runif(11 * 11));
> colnames(x) <- paste('col', 1:11, sep = '-');
> rownames(x) <- paste('row', 1:11, sep = '-');
>
> # Create some covariate data
> covariate.colours <- x[,1]
> covariate.colours[covariate.colours >= 0] <-
"cornflowerblue";
> covariate.colours[covariate.colours != "cornflowerblue"] <-
"coral";
>
> covariates <-list(
+ rect = list(
+ col = "black",
+ fill = covariate.colours,
+ lwd = 1.5
+ )
+ );>
>
> # Cluster the data
> dd <- hclust(dist(x, method = "canberra"));
> dd <- as.dendrogram(dd);
>
> levelplot(
+ t(x),
+ scales = list(
+ x = list(
+ rot = 90
+ )
+ ),
+ colorkey = FALSE,
+ legend = list(
+ right = list(
+ fun = latticeExtra::dendrogramGrob,
+ args = list(
+ x = dd,
+ ord = order.dendrogram(dd),
+ side = "right",
+ size = 2.5,
+ size.add = 1,
+ add = covariates,
+ type = "rectangle"
+ )
+ )
+ )
+ );
In the resulting plot (attached as
'dendrogramGrob_covariates_example.png'), the bottom branches of the
dendrogram are indistinguishable from the edge of the covariate bar.
I've been able to solve the problem by using my own version of
dendrogramGrob that inserts a narrow extra grid column between the bar and the
dendrogram in order to add whitespace (attached as
'dendrogramGrob_covariates_example_with_space.png'). Perhaps the actual
dendrogramGrob function could be edited so that whitespace can be added between
the rectangles and the dendrograms if desired?
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] latticeExtra_0.6-20 RColorBrewer_1.0-5 lattice_0.20-6
loaded via a namespace (and not attached):
[1] tools_2.14.2
Thanks,
Lauren Chong
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dendrogramGrob_covariates_example.png
Type: image/png
Size: 217429 bytes
Desc: dendrogramGrob_covariates_example.png
URL:
<https://stat.ethz.ch/pipermail/r-help/attachments/20120403/025232e1/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dendrogramGrob_covariates_example_with_space.png
Type: image/png
Size: 219093 bytes
Desc: dendrogramGrob_covariates_example_with_space.png
URL:
<https://stat.ethz.ch/pipermail/r-help/attachments/20120403/025232e1/attachment-0003.png>
