Entering edit mode
8 weeks ago
Hann
▴
110
Hello,
I have generated a figure of phylogenetic tree. This is my R script to generate phylogenetic tree. However, I would like to add different shapes as a lable (in the tree tip) not only one shape as it's now.
These shapes are from ploly R library as ggplot shapes are not enough for my dataset. I could not use shapes in ggplot2 as I need a lot of shapes so best options is plotly (I have generated PCA and other plots with the same shapes, so it's also to be consistent). See below file has the shapes.
# Load necessary libraries
library("ape")
library("ggtree")
library("plotly")
library(data.table)
# Replace these with your file paths
tree<-read.newick("minCov8_minmeanDP0_maxmissing0.8_remove_contaminatedIndvs_removeDupindvs_ldpruned_maf0.05_removePRZW221kb.boot_reroot.nwk")
#pdf("tree_test2.pdf", width = 15, height =80, pointsize = 1/300)
p <- ggtree(tree,layout="rectangular",size=0.1,ladderize=T)# +geom_tiplab(aes(label=label),size=2)
p
##get the tip labels to give colours, ordered as the tree
ladder<- ladderize(tree, right = FALSE)
is_tip <- ladder$edge[,2] <= length(ladder$tip.label)
ordered_tips <- ladder$edge[is_tip, 2]
names<-data.frame(ladder$tip.label[ordered_tips])
#make the colours for each tip
ETH5B<-rep("black", 1)
PRZW16<-rep("black", 1)
PRZW17<-rep("black", 1)
PRZW15<-rep("black", 1)
PRZW14<-rep("black", 1)
PRZW11<-rep("black", 1)
PRZW29<-rep("black", 1)
PRZW19<-rep("black", 1)
PRZW18<-rep("black", 1)
PRZW20<-rep("black", 1)
PRZW21<-rep("black", 1)
PRZW12<-rep("black", 1)
PRZW10<-rep("black", 1)
PRZW23<-rep("black", 1)
PRZW22<-rep("black", 1)
PRZW2<-rep("black", 1)
PRZW30<-rep("black", 1)
PRZW31<-rep("black", 1)
PRZW13<-rep("black", 1)
PRZW4<-rep("black", 1)
PRZW9<-rep("black", 1)
PRZW5<-rep("black", 1)
PRZW8<-rep("black", 1)
PRZW3<-rep("black", 1)
PRZW7<-rep("black", 1)
PRZW6<-rep("black", 1)
PRZW1<-rep("black", 1)
MONG8<-rep("palevioletred3", 1)
TSHU2<-rep("lightpink1", 1)
TSHU1<-rep("lightpink1", 1)
NOMA2<-rep("lightpink1", 1)
NOMA1<-rep("lightpink1", 1)
KISO2<-rep("lightpink1", 1)
KISO1<-rep("lightpink1", 1)
HOKK2<-rep("lightpink1", 1)
HOKK1<-rep("lightpink1", 1)
MISA2<-rep("lightpink1", 1)
MISA1<-rep("lightpink1", 1)
TOKA2<-rep("lightpink1", 1)
TOKA1<-rep("lightpink1", 1)
YONA2<-rep("lightpink1", 1)
YONA1<-rep("lightpink1", 1)
MIYA2<-rep("lightpink1", 1)
MIYA1<-rep("lightpink1", 1)
...etc
#merge together
colours<-c(
ETH5B,PRZW16,PRZW17,PRZW15,PRZW14,PRZW11,PRZW29,PRZW19,PRZW18,PRZW20,PRZW21,PRZW12,PRZW10,PRZW23,PRZW22,PRZW2,PRZW30,PRZW31,PRZW13,PRZW4,PRZW9,PRZW5,PRZW8,PRZW3,PRZW7,PRZW6,PRZW1,
MONG8,TSHU2,TSHU1,NOMA2,NOMA1,KISO2,KISO1,HOKK2,HOKK1,MISA2,MISA1,TOKA2,TOKA1,YONA2,YONA1,MIYA2,MIYA1 ...etc
)
tips<-data.frame(names,colours)
tips$family<-sub("\\_.*", "", tips$ladder.tip.label.ordered_tips.)
str(tips)
##add colours and tips into tree
tip.tree<-p %<+% tips + geom_tippoint(aes(colour=colours), shape=1, size=0.8) + # .... I need help here. I do not want one shape. I have the sapes in a table (see below) and I would like to use the same shapes for each tip name in the tree ... Shapes are from plotly R package. So I need to find a way to add plotly shapes to ggplot2
scale_colour_manual(breaks =tips$colours,values=tips$colours) +
theme(legend.position="none")
tip.tree
#add in bootstraps
q <- ggtree(tree)
d <- q$data
d <- d[!d$isTip,]
d$label <- as.numeric(d$label)
d <- d[d$label > 90,]
d
tree<-tip.tree + geom_point(data=d,aes(node=node),shape=16, size=.4, fill='black',stat="identity") +
theme(plot.margin = unit(c(0.15,0,0.8,0), "cm")) +
geom_treescale(x=0, y=350,width=0.02, color='black',offset=5) +
xlim(0, 0.3)
tree
tree+ geom_text(aes(label=node), hjust=-.3)
## I found that to add options to the plot, first convert ggplot2 plot to Plotly variable with ggplotly() and then, add options to that variable.
fig <- ggplotly(tree) fig <- fig %>% # ..... But I do not think in this case is possible
data frame with the shapes:
shapes <-fread("names_shapes.txt")
names shapes ETH5B circle PRZW16 circle-open PRZW17 circle-open
PRZW15 circle-open PRZW14 circle-open PRZW11 circle-open
PRZW29 circle-open PRZW19 circle-open PRZW18 circle-open
PRZW20 circle-open PRZW21 circle-open PRZW12 circle-open
PRZW10 circle-open PRZW23 circle-open PRZW22 circle-open
PRZW2 circle-open PRZW30 circle-open PRZW31 circle-open
PRZW13 circle-open PRZW4 circle-open PRZW9 circle-open
PRZW5 circle-open PRZW8 circle-open PRZW3 circle-open
PRZW7 circle-open PRZW6 circle-open PRZW1 circle-open MONG8 x-open
TSHU2 diamond-tall TSHU1 diamond-tall NOMA2 x NOMA1 x
KISO2 diamond-cross-open KISO1 diamond-cross-open
HOKK2 triangle-up-open HOKK1 triangle-up-open MISA2 diamond-wide
MISA1 diamond-wide TOKA2 cross-open TOKA1 cross-open
YONA2 star-diamond YONA1 star-diamond MIYA2 cross MIYA1 cross
..
..
My current phylogenetic tree look like this (one shape on the tips). I would greatly appreciate your input and help. Thanks!
