I am trying to plot an edge bundling graph in R with ggraph
using geom_conn_bundle
and I'm having a hard time trying to figure out why the color mappings aren't working properly.
I have a data frame with 152 rows and 3 columns: from, to, and color. Each row represents a connection between two people.
I used this tutorial to build my main plotting function:
Here is the code:
data_df <- read.csv('Final Natarajan - CGMRP_CCSG-Pubs_Fig-1-2.csv')
data_df_color_mapping <- data_df$color
data_df_color_mapping <- data_df_color_mapping[!(duplicated(data_df))]
data_df <- data_df[!(duplicated(data_df)),]
row.names(data_df) <- NULL
colnames(data_df) <- c('from', 'to')
hierarchy <- data.frame('from' = rep('origin', 71), 'to' = unique(c(as.character(data_df$from),
as.character(data_df$to))))
vertices <- data.frame(name = unique(c(as.character(hierarchy$from), as.character(hierarchy$to))) )
mygraph <- graph_from_data_frame( hierarchy, vertices=vertices )
# The connection object must refer to the ids of the leaves:
from <- match( data_df$from, vertices$name)
to <- match( data_df$to, vertices$name)
vertices$id <- NA
myleaves <- which(is.na( match(vertices$name, hierarchy$from) ))
nleaves <- length(myleaves)
vertices$id[ myleaves ] <- seq(1:leaves)
vertices$angle <- 110 - 360 * vertices$id / leaves
# calculate the alignment of labels: right or left
# If I am on the left part of the plot, my labels have currently an angle < -90
vertices$hjust <- ifelse( vertices$angle < -90, 1, 0)
# flip angle BY to make them readable
vertices$angle <- ifelse(vertices$angle < -90, vertices$angle+180, vertices$angle)
png(file="edge_bundle.png",width=360*10,height=335*10)
ggraph(mygraph, layout = 'dendrogram', circular = TRUE) +
geom_conn_bundle(data = get_con(from = from, to = to), color=data_df_color_mapping,
alpha=.3, width=2) +
geom_node_text(aes(x = x*1.12, y=y*1.12, filter = leaf, label=name, angle=vertices$angle), size=16,
alpha=1) +
theme_void() +
theme(
legend.position="none",
plot.margin=unit(c(0,0,0,0),"cm"),
) +
expand_limits(x = c(-1.2, 1.2), y = c(-1.2, 1.2))
dev.off()
I have an issue with
geom_conn_bundle(data = get_con(from = from, to = to), color=data_df_color_mapping,
alpha=.3, width=2)
I get the following error:
Error: Aesthetics must be either length 1 or the same as the data (15200): edge_colour
I fix it with color=rep(data_df_color_mapping, each=100)
but the mapping is off. I can't figure out the pattern. I naturally assumed that I have to repeat each color 100 times since I have 152 rows but it doesn't work like that.
I also have a problem with putting color inside aes()
, in that case I get the following error
Error: Aesthetics must be either length 1 or the same as the data (456): edge_colour
Now it's 3 times more data points than I have in my data frame.
Can anyone please help me understand how the get_con() function works or help me figure out how to pass the edge color data.
Thanks!
EDIT: The .csv file
The image it generates when I fix it with color=rep(data_df_color_mapping, each=100)
I figured it out randomly. So when I reordered the data, I forgot to change the color mapping and I realized that it produced the same plot. So what happens is that it orders the graph according to the vertex index of "from". When I order my graph beforehand, it produces the desired result.