gheatmap binary data

[Breanna Sipley]

Hi there,

I have a circular tree & presence/absence data for each tip.  I would like to map this data onto my tree.  

I have followed the tutorial at https://rgriff23.github.io/2017/05/11/primate-phylogeny-ggtree.html & have seen https://github.com/GuangchuangYu/ggtree/issues/78#issuecomment-252172314, but am still having problems.  

It seems my code generates the skeleton of the map but does not successfully populate it. 

Here's my code:

tree <- read.tree("tree.tre")
dd <- read.csv("data.txt",
                sep = "\t",
                col.names = c("tipLabel", "dat"),
                header = FALSE,
                stringsAsFactors = TRUE)
dd.sub <- subset(dd, tipLabel %in% tree$tip.label)
dd.sub$dat <- ifelse(dd.sub$dat=="YES","present","absent")
row.names(dd.sub) <- NULL

circ <- ggtree(tree, layout="circular", branch.length = "none")
p <- gheatmap(circ, dd.sub["dat"], offset=0.1, width=0.02,
              low="salmon",high="black", color="purple") +
  scale_fill_manual(values=c("salmon","black")) +
  coord_polar(theta='y')

png("error.png")
plot(p)
dev.off()

Which returns this:

Some more info:

# I'm pretty sure I've set up my dataframe ok

> head(dd.sub["dat"])
      dat
1 present
2  absent
3 present
4  absent
5  absent
6  absent

# Data consists of "present" or "absent" only

> summary(factor(dd.sub$dat))
 absent present
     88     185

# There's a 1:1 between my tips & binary data

> summary(dd.sub$tipLabel %in% tree$tip.label)
   Mode    TRUE
logical     273

Any advice?

Cheers,

Breanna

[Yu, Guangchuang]

any reproducible example? If you want to keep your data confidential, you can send the file to me instead of posting on the group.

--
G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
 
Homepage: https://guangchuangyu.github.io/software/ggtree
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--

--~--~---------~--~----~------------~-------~--~----~

Guangchuang Yu PhD

Postdoc researcher
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

-~----------~----~----~----~------~----~------~--~---

[Yu, Guangchuang]

maybe you should try color = NULL to disable drawing cell borders. It seems that the color we can see on the plot are all ‘purple` that you specifying for the cell border.

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