I've created a circular dendogram using R and the ggraph package. I have my labels and nodes correctly colored by "group". However, I'm unsure how to color the lines by "colors" (my color column). Currently I can change the line color to a single color (e.g. "red"), though I can't color them dynamically by column "colors".
My code is based on code from the r-graph gallery website. As you can see from my datafiles, I've tried adding a "colors" column and then calling that in my ggraph call but that gives me the following error:
Error in `geom_edge_diagonal(colour = colors)`:
! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `rep()`:
! attempt to replicate an object of type 'closure'
Here is my code:
library(ggraph)
library(igraph)
library(tidyverse)
library(RColorBrewer)
d1 = read.csv("~/data1.csv", sep=",")
d2 = read.csv("~/data2.csv", sep=",")
edges=rbind(d1, d2)
# create a vertices data.frame. One line per object of our hierarchy
vertices = data.frame(
name = unique(c(as.character(edges$from), as.character(edges$to))) ,
value = runif(78)
)
# Let's add a column with the group of each name. It will be useful later to color points
vertices$group = edges$from[ match( vertices$name, edges$to, edges$colors ) ]
#Let's add information concerning the label we are going to add: angle, horizontal adjustement and potential flip
#calculate the ANGLE of the labels
vertices$id=NA
myleaves=which(is.na( match(vertices$name, edges$from, edges$colors) ))
nleaves=length(myleaves)
vertices$id[ myleaves ] = seq(1:nleaves)
vertices$angle= 90 - 360 * vertices$id / nleaves
# calculate the alignment of labels: right or left
# If I am on the left part of the plot, my labels have currently an angle < -90
vertices$hjust<-ifelse( vertices$angle < -90, 1, 0)
# flip angle BY to make them readable
vertices$angle<-ifelse(vertices$angle < -90, vertices$angle+180, vertices$angle)
# Create a graph object
mygraph <- graph_from_data_frame( edges, vertices=vertices )
# Make the plot
ggraph(mygraph, layout = 'dendrogram', circular = TRUE) +
geom_edge_diagonal(colour=colors) +
scale_edge_colour_distiller(palette = "RdPu") +
geom_node_text(aes(x = x*1.12, y=y*1.12, filter = leaf, label=name, angle = angle, colour=group, hjust=hjust), size=6) +
geom_node_point(aes(filter = leaf, x = x*1.07, y=y*1.07, colour=group, alpha=.2, size=2)) +
scale_colour_manual(values= rep( brewer.pal(7,"Paired") , 30)) +
scale_size_continuous( range = c(0.1,17) ) +
theme_void() +
theme(
legend.position="none",
plot.margin=unit(c(0,0,0,0),"cm"),
) +
expand_limits(x = c(-1.3, 1.3), y = c(-1.3, 1.3))
Here are two minimal examples of the code used:
data1.csv
from,to,colors
origin,group1,color1
origin,group2,color1
origin,group3,color1
origin,group4,color2
origin,group5,color2
origin,group6,color3
origin,group7,color3
origin,group8,color4
origin,group9,color4
data2.csv
from,to,colors
group1,"test1",color1
group2,"test2",color1
group3,"test3",color1
group4,"test4",color2
group5,"test5",color2
group6,"test6",color3
group7,"test7",color3
group8,"test8",color4
group9,"test9",color4
I believe the following line is the one I need help with (inside my ggraph call):
geom_edge_diagonal(colour=colors) +
If it helps, my question is the same as asking how to color lines by group on the example code I used, taken from r-graph gallery.
Any help is appreciated.
