Bug in gplot.heatmap about ggtree

[GuangchuangYu]

Good catch and thanks for your report. The reorder issue has been removed in ggtree (version >=0.99.18).

For the line up issue, since that can't be supported internally in current version of ggplot2 (please refer to the Linked micromaps section in ggplot2's wishlist feature requests), gplot will output a list of ggplot2 objects and user can manual adjust them if they can't be aligned properly.

Of course, I will explore some possibilities to align them more accurately.

[mworkentine]

Thanks for the quick fix!

As for the alignment issue I did find that adding scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0)) to the tree plot allowed for better alignment.

[GuangchuangYu]

In devel branch, I have created another function called gheatmap, will will always line up the heatmap to the tree properly.

please refer to the new vignette: http://www.bioconductor.org/packages/3.2/bioc/vignettes/ggtree/inst/doc/ggtree.html