How to remove NA in the legend?

[zhan xw]

Hello,

Following ggtree documentation codes as following, I wonder how to hide "NA" from the figure legend(see attached).

Any suggestions? Thanks.

library(ggtree)
nwk <- system.file("extdata", "sample.nwk", package="treeio")
tree <- read.tree(nwk)
p <- ggtree(tree)


dd <- data.frame(taxa  = LETTERS[1:13],
                 place = c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
                 value = round(abs(rnorm(13, mean=70, sd=10)), digits=1))
## you don't need to order the data
## data was reshuffled just for demonstration
dd <- dd[sample(1:13, 13), ]
row.names(dd) <- NULL
print(dd)


p <- p %<+% dd + geom_tiplab(aes(color=place)) +
  geom_tippoint(aes(size=value, shape=place, color=place), alpha=0.25)
p + theme(legend.position="right")

[Yu, Guangchuang]

use `scale_color_manual` to set the `breaks` that exclude `NA`.

--
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

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

[Xiaowei Zhan]

Your solution works now:

Use: 

p + theme(legend.position="right") + scale_color_manual(values = c("red", "blue", "green"), breaks=c("CZ", "GZ", "HK")) + scale_shape_manual(values = seq(3), breaks=c("CZ", "GZ", "HK"))

Instead of:

p + theme(legend.position="right")

Thanks. 

Best,

Xiaowei

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