ggtree facet_plot question using geom_boxplot to plot abundance data corresponding to tree tips
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@matthewwipperman-12544
Last seen 4.6 years ago
New York City

Hello,

I have a question about how to add a horizontal bar graph to a ggtree object. I would like to merge a ggtree object with a geom_boxplot object, where the abundances in the boxplot correspond to taxa on the ggtree tips. My understanding is that the facet_plot function would be ideal for this, but I have tried pretty hard and can't seem to get it to work. A reproducible example of what I can (and can't do) is attached using the Phyloseq package in the R environment. 

I am sure there are other ways to do this, so this i just a rough skelton

There are different groups of abundance values for the facet_plot 'barploth' function, but they will not plot using this function, even though the data is there. Even if the tip names are unique, I am unable to get this to work. Happy to answer any other questions, and thanks in advance for the help! --Matt

 

#!usr/bin/env RScript

rm (list = ls())
library(phyloseq);library(ggstance);library(ggthemes);library(plyr);library(dplyr)
library(ggtree);library(tibble)

#load sample Phyloseq dataset
data("GlobalPatterns")
GP <- GlobalPatterns
GP <- prune_taxa(taxa_sums(GP) > 500, GP)
humantypes <- c("Feces", "Skin") #make it a bit simpler 
sample_data(GP)$human <- get_variable(GP, "SampleType") %in% humantypes

mergedGP <- merge_samples(GP, "SampleType")
mergedGP <- rarefy_even_depth(mergedGP,rngseed=394582)
mergedGP <- tax_glom(mergedGP,"Order") #make the tree smaller for the purposes of this example

print(mergedGP) #final phyloseq object

#make a tree
tr <- phy_tree(mergedGP)
spec <- tax_table(mergedGP) %>% data.frame(stringsAsFactors = FALSE) %>% tibble::rownames_to_column("otu")
gt <- ggtree(tr, branch.length = "y") %<+% spec 
gd <- gt$data

melt_data<-psmelt(mergedGP) 

tt <- melt_data%>%left_join(select(gd,OTU=label,x,y),by="OTU") %>%
  arrange(Sample) %>%  mutate(sample2=factor(Sample,levels=unique(Sample)),
  col=as.numeric(sample2),x.col=scales::rescale(col,to=c(1.3,2)))

#this will demonstrate that one can make a ggtree object with abundance data (other examples show this tpp)
g <- gt + geom_tippoint(data=gd$istip,aes(color=Phylum),size=2) + 
  geom_text(data=gd$istip,aes(label=Genus,x=x+0.01,size='smaller[1]'),hjust=0.1,check_overlap = T)+ 
  geom_tile(data=tt,aes(x=x.col,y=y,fill=Sample,alpha=Abundance)) +
  theme(legend.position="right") #+ geom_tiplab2()
g

#make a simple dataframe to build the boxplots
melt_simple <- subset(melt_data,select=c(OTU,Sample,Abundance))

#this just makes a simple tree
g.left <- gt + geom_tippoint(data=gd$istip,aes(color=Class),size=2) +
  geom_text(data=gd$istip,aes(label=Genus,x=x+0.01,size='smaller[1]'),hjust=0.1,check_overlap = T) 
g.left

#This function will produce the boxplot that I want, with boxes for each sample on the right side corresponding to that tree tip
ggplot(melt_simple,aes(x=OTU,y=Abundance))+ 
  geom_boxplot(position=position_dodge(),colour="black",size=.3,alpha=0.5) + 
  scale_color_manual() + 
  scale_fill_manual() +  coord_flip() + 
  scale_y_continuous(limits = c(0,300))

###code works until here###

#This is the step where I have an error
facet_plot(g.left, panel="Boxplot", data=melt_simple, geom_boxploth, 
           mapping = aes(x=Abundance,group=label,color="377eb8"),
           outlier.shape=NA) 

ggtree ggplot2 phyloseq geom_boxplot facet_plot • 1.2k views
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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

don’t copy-past your question to multiple places. Your question had already answered in https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/RgI8M4DDBT8/7Kp-hyNqAQAJ.

This thread should be closed.

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