Map traits at tips in different color palettes
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Edeline Gagnon
Apr 5, 2018, 6:24:47 PM4/5/18
to ggtree
Hello,
I have three qualitative traits that I would to represent at the tip of a phylogenetic tree.
I've managed to figure out how each trait could be represented by a different shape, but I would also like to be able to select different color palettes for each trait, to make it easier to read the figure.
I suspect the answer lies somewhere with scale_color_manually, but so far I haven't been able to sort it out complete. It looks as if I have to manually specify each color.
Any help to tweak this code would be appreciated.
I've included a figure of the tree i've managed to produce so far, along with my R script, and a sample of the data I'm using.
Thanks in advance!
With best regards,
Edeline
#Import tree file, as well as trait data for tips of tree.
tree2 <-read.beast(file.choose())
dd <- read.csv(file.choose())
p <- ggtree(tree2, ladderize=TRUE) +
# Add posterior probability
geom_text2(aes(subset=!isTip, label=round(as.numeric(posterior),2)),size=1.5, hjust=-.3, vjust=-.5) +
# geom_text2(aes(subset=posterior<0.7, label=round(as.numeric(posterior),2)),size=1.5, hjust=-.3, vjust=-.5) +
# Adds tip labels
geom_tiplab(color="black",size=1.5, offset=3) +
#This ensures that there will be space in the plot.
xlim(0, 80)+
# Adds an axis
theme_tree2() +
# Add point where mezoneuron fossil is MRCA(tre3,mezo) = 324
geom_point2(aes(subset=(node ==324) ),size=2, shape=24, fill="steelblue")
p2 <- p %<+% dd +
geom_tippoint(aes(x=x+0.5,fill = factor(Biome)),shape=21,size=2) +
geom_tippoint(aes(x=x+1.5,fill = factor(Habit)),shape=23,size=2) +
geom_tippoint(aes(x=x+2.5,fill = factor(Geo)),shape=22,size=2)
#uncomment if you want to see the legend + theme(legend.position="right",legend.key.size = ) + scale_color_brewer(palette=2)
#suspect that this is where I would need to use scale_color_manually, but not sure how....
p2
I have three qualitative traits that I would to represent at the tip of a phylogenetic tree.
I've managed to figure out how each trait could be represented by a different shape, but I would also like to be able to select different color palettes for each trait, to make it easier to read the figure.
I suspect the answer lies somewhere with scale_color_manually, but so far I haven't been able to sort it out complete. It looks as if I have to manually specify each color.
Any help to tweak this code would be appreciated.
I've included a figure of the tree i've managed to produce so far, along with my R script, and a sample of the data I'm using.
Thanks in advance!
With best regards,
Edeline
#Import tree file, as well as trait data for tips of tree.
tree2 <-read.beast(file.choose())
dd <- read.csv(file.choose())
p <- ggtree(tree2, ladderize=TRUE) +
# Add posterior probability
geom_text2(aes(subset=!isTip, label=round(as.numeric(posterior),2)),size=1.5, hjust=-.3, vjust=-.5) +
# geom_text2(aes(subset=posterior<0.7, label=round(as.numeric(posterior),2)),size=1.5, hjust=-.3, vjust=-.5) +
# Adds tip labels
geom_tiplab(color="black",size=1.5, offset=3) +
#This ensures that there will be space in the plot.
xlim(0, 80)+
# Adds an axis
theme_tree2() +
# Add point where mezoneuron fossil is MRCA(tre3,mezo) = 324
geom_point2(aes(subset=(node ==324) ),size=2, shape=24, fill="steelblue")
p2 <- p %<+% dd +
geom_tippoint(aes(x=x+0.5,fill = factor(Biome)),shape=21,size=2) +
geom_tippoint(aes(x=x+1.5,fill = factor(Habit)),shape=23,size=2) +
geom_tippoint(aes(x=x+2.5,fill = factor(Geo)),shape=22,size=2)
#uncomment if you want to see the legend + theme(legend.position="right",legend.key.size = ) + scale_color_brewer(palette=2)
#suspect that this is where I would need to use scale_color_manually, but not sure how....
p2
Yu, Guangchuang
Apr 11, 2018, 2:49:19 AM4/11/18
to Edeline Gagnon, ggtree
You can try something similar to https://github.com/GuangchuangYu/ggtree/issues/78#issuecomment-252172314.
--
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
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
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