I made a phylogenetic tree plot with the igraph package.
The problem is, that my tree is too big to fit into the saved image.
I'm using Rstudio and usually saving my plots manually.
With smaller trees, I was able to enlarge the plot window of Rstudio to make the plot fit into the image, without the nodes overlapping each other.
Unfortunately, this isn't working with my latest plot.
I tried to save it with png(), pdf() and jpeg() with different width and height, but it still doesn't fit properly.
Either the nodes overlap each other or only a part of the plot is visible in the image.
The only solution I found so far was to decrease the label size. But in the end, you can't read anything.
Thank you in advance for your help.
Here is my code:
id <- c("Spirochaetota","Brachyspirae","Brevinematia","Leptospirae","Spirochaetia","sk6","Brachyspirales","Brachyspiraceae","Brachyspira",
"Brevinematales","bo1","Brevinemataceae","Brevinema","bf2","Leptospirales","Leptonemataceae","Leptonema","lg2","Leptospiraceae","Leptospira",
"LeptospiraA","LeptospiraB","lg3","lf1","Turneriellales","Turneriellaceae","Turneriella","tf1","Borreliales","Borreliaceae","Borrelia",
"Borreliella","Sphaerochaetales","Sphaerrochaetaceae","Sphaerochaeta","SphaerochaetaA","sg15","SpirochaetalesA","SpirochaetaceaeA",
"SpirochaetaA","sf1","SpirochaetalesC","Alkalispirochaetaceae","Alkalispirochaeta","Salinispiraceae","Salinispira","SpirochaetaD","sg1",
"sf6","SpirochaetalesD","sdf1","SpirochaetalesE","SpirochaetaceaeB","Oceanispirochaeta","SpirochaetaE","SpirochaetaF","SpirochaetaG","sg2",
"Treponematales","Treponemataceae","Treponema","TreponemaB","TreponemaC","TreponemaD","TreponemaF","tg7","TreponemataceaeB","TreponemaE",
"TreponemaG","TreponemaH","tg5","tf3","so11")
links <- data.frame(from = c("Spirochaetota","Spirochaetota","Spirochaetota","Spirochaetota","Spirochaetota","Brachyspirae",
"Brachyspirales","Brachyspiraceae","Brevinematia","Brevinematia","Brevinematales","Brevinemataceae",
"Brevinematales","Leptospirae","Leptospirales","Leptonemataceae","Leptonemataceae","Leptospirales",
"Leptospiraceae","Leptospiraceae","Leptospiraceae","Leptospiraceae","Leptospirales","Leptospirae",
"Turneriellales","Turneriellaceae","Turneriellales","Spirochaetia","Borreliales","Borreliaceae",
"Borreliaceae","Spirochaetia","Sphaerochaetales","Sphaerrochaetaceae","Sphaerrochaetaceae","Sphaerrochaetaceae",
"Spirochaetia","SpirochaetalesA","SpirochaetaceaeA","SpirochaetalesA","Spirochaetia","SpirochaetalesC",
"Alkalispirochaetaceae","SpirochaetalesC","Salinispiraceae","Salinispiraceae","Salinispiraceae","SpirochaetalesC",
"Spirochaetia","SpirochaetalesD","Spirochaetia","SpirochaetalesE","SpirochaetaceaeB","SpirochaetaceaeB",
"SpirochaetaceaeB","SpirochaetaceaeB","SpirochaetaceaeB","Spirochaetia","Treponematales","Treponemataceae",
"Treponemataceae","Treponemataceae","Treponemataceae","Treponemataceae","Treponemataceae","Treponematales",
"TreponemataceaeB","TreponemataceaeB","TreponemataceaeB","TreponemataceaeB","Treponematales","Spirochaetia"),
to = c("Brachyspirae","Brevinematia","Leptospirae","Spirochaetia","sk6","Brachyspirales",
"Brachyspiraceae","Brachyspira","Brevinematales","bo1","Brevinemataceae","Brevinema",
"bf2","Leptospirales","Leptonemataceae","Leptonema","lg2","Leptospiraceae",
"Leptospira","LeptospiraA","LeptospiraB","lg3","lf1","Turneriellales",
"Turneriellaceae","Turneriella","tf1","Borreliales","Borreliaceae","Borrelia",
"Borreliella","Sphaerochaetales","Sphaerrochaetaceae","Sphaerochaeta","SphaerochaetaA","sg15",
"SpirochaetalesA","SpirochaetaceaeA","SpirochaetaA","sf1","SpirochaetalesC","Alkalispirochaetaceae",
"Alkalispirochaeta","Salinispiraceae","Salinispira","SpirochaetaD","sg1","sf6",
"SpirochaetalesD","sdf1","SpirochaetalesE","SpirochaetaceaeB","Oceanispirochaeta","SpirochaetaE",
"SpirochaetaF","SpirochaetaG","sg2","Treponematales","Treponemataceae","Treponema",
"TreponemaB","TreponemaC","TreponemaD","TreponemaF","tg7","TreponemataceaeB",
"TreponemaE","TreponemaG","TreponemaH","tg5","tf3","so11"))
net <- graph_from_data_frame(d = links, vertices = id, directed = T)
lay = layout.reingold.tilford(net)
plot(net, vertex.shape = "none",
vertex.label.font = 3,
vertex.label.cex = 0.3,
edge.arrow.size = 0.3,
rescale = F,
ylim = c(0.7,3.4),xlim = c(-8,23.2), asp = 0,
layout = lay)
If everything works, it should look similar to this smaller tree. this one does not include the nodes of the code above:
This is my result of the big tree so far. It contains the nodes in the code above:
The only solution I came up with so far is to somehow fit the plot into the plot panel and save it as a SVG file. Afterwards, I edited it using inkscape:
You can plot the tree graph as a dendrogram.
Drawing it left to right allows to put all of the taxon labels in a readable column:
library(igraph)
net <- graph_from_data_frame(d = links, vertices = id, directed = F)
lay <- layout.reingold.tilford(net)
plot_dendrogram(cluster_fast_greedy(net))
There is also:
links %>%
graph_from_data_frame() %>%
as_adjacency_matrix() %>%
dist() %>%
hclust() %>%
as.dendrogram() %>%
plot()
I am trying to draw a standard triangular mediation diagram using DiagrammeR in R (it can also interpret graphviz code). On the whole, it's working fine but the edge label text gets placed oddly. The bottom edge label is not centered and the two angled edge labels are positioned at different heights (see the red lines in the diagram below). Is there a way to manually assign positions to edge text or get something more consistent?`
library(DiagrammeR)
# Create a node data frame (ndf)
ndf <- create_node_df(
n = 3,
label = c("Experimental\nTreatment", "Some\nMediator", "Outcome\nof Interest"),
shape = rep("rectangle", 3),
style = "empty",
fontsize = 6,
fixedsize = TRUE,
height = .5,
width = .75,
color = "gray40",
x = c(1, 2, 3),
y = c(1, 2, 1)
)
# Create an edge data frame (edf)
edf <- create_edge_df(
from = c(1, 1, 2),
to = c(2, 3, 3),
label = c("1.1*", "2.0*", "-0.33***"),
fontsize = 6,
minlen = 1,
color = "gray40",
)
# Create a graph with the ndf and edf
graph <- create_graph(
nodes_df = ndf,
edges_df = edf
)
graph %>%
render_graph()
I would also love to know the answer to this.
I have tried to delete the default "layout" graph attribute and set direction of graph layout via:
graphAttr <- DiagrammeR::get_global_graph_attrs(graph)
But, I get the following error:
Error: 'get_global_graph_attrs' is not an exported object from 'namespace:DiagrammeR'
....which it is, consequently, I am stuck.
After fiddling with DiagrammeR for a while, I ended up switching to the LaTeX diagramming package TikZ. It allows for enormous control of every aspect of the diagram but can be overwhelming. TikZ would require a bit of tweaking, also, to get diagrams into HTML output if that's important. For a presentation using LaTeX's Beamer class for slides, generating TikZ code with a function in R worked well. That TikZ code was then written to a text file that could be imported automatically via the LaTeX command \input{path/to/file.txt} or just copied and pasted into my slides.
See the code for two DiagrammeR solutions and the TikZ solution, here: https://stackoverflow.com/a/64886536/893399
I'm using visNetwork in R to generate a hierarchal network map. I want the paths of which get highlighted upon node selection to follow a user-defined rule (EG, adding to the dataset.) Please follow my example below.
library(tidyverse)
library(visNetwork)
nodes = data.frame(id = 1:7, level = c(1, 2, 3, 3, 4, 2,1))
edges = data.frame(from = c(1, 2, 2, 4, 6,7,7), to = c(2, 3, 4, 5, 4,6,2))
visNetwork(nodes, edges) %>%
visHierarchicalLayout() %>%
visEdges(arrows = "to") %>%
visOptions(highlightNearest = list(enabled = TRUE, algorithm = "hierarchical",
degree = n_distinct(nodes$level))) %>%
visHierarchicalLayout(direction = "DU")
This code produces the below network map
When selecting node 1, I get the left picture below; When selecting node 7, i get the right picture below. IE, the highlighting follows all the arrows to the top.
I want to find a way in which I can add to the nodes/edges data to user-define the behaviour of the highlighting? EG, when selecting 7 (in the diagram on the right above), it excludes highlighting 2 and 3.
I see two possible options:
1. Adding to the data so that it produces two types of edges; 1 that is just for show and the other that's used for highlighting paths as well being shown.
2. Add extra columns to the data so that it somehow knows how to path highlighting when selecting each node
Open to other suggestions on the options or even packages.
Thanks
I am building a phylogenetic tree using data from NCBI taxonomy. The tree is quite simple, its aims is to show the relationship among a few Arthropods.
The problem is the tree looks very small and I can't seem to make its branches longer. I would also like to color some nodes (Ex: Pancrustaceans) but I don't know how to do this using ape.
Thanks for any help!
library(treeio)
library(ape)
treeText <- readLines('phyliptree.phy')
treeText <- paste0(treeText, collapse="")
tree <- read.tree(text = treeText) ## load tree
distMat <- cophenetic(tree) ## generate dist matrix
plot(tree, use.edge.length = TRUE,show.node.label = T, edge.width = 2, label.offset = 0.75, type = "cladogram", cex = 1, lwd=2)
Here are some pointers using the ape package. I am using a random tree as we don't have access to yours, but these examples should be easily adaptable to your problem. If your provide a reproducible example of a specific question, I could take another look.
First me make a random tree, add some species names, and plot it to show the numbers of nodes (both terminal and internal)
library(ape)
set.seed(123)
Tree <- rtree(10)
Tree$tip.label <- paste("Species", 1:10, sep="_")
plot.phylo(Tree)
nodelabels() # blue
tiplabels() # yellow
edgelabels() # green
Then, to color any node or edge of the tree, we can create a vector of colors and provide it to the appropriate *labels() function.
# using numbers for colors
node_colors <- rep(5:6, each=5)[1:9] # 9 internal nodes
edge_colors <- rep(3:4, each=9) # 18 branches
tip_colors <- rep(c(11,12,13), 4)
# plot:
plot.phylo(Tree, edge.color = edge_colors, tip.color = tip_colors)
nodelabels(pch = 21, bg = node_colors, cex=2)
To label just one node and the clade descending from it, we could do:
Nnode(Tree)
node_colors <- rep(NA, 9)
node_colors[7] <- "green"
node_shape <- ifelse(is.na(node_colors), NA, 21)
edge_colors <- rep("black", 18)
edge_colors[13:18] <- "green"
plot(Tree, edge.color = edge_colors, edge.width = 2, label.offset = .1)
nodelabels(pch=node_shape, bg=node_colors, cex=2)
Without your tree, it is harder to tell how to adjust the branches. One way is to reduce the size of the tip labels, so they take up less space. Another way might be to play around when saving the png or pdf.
There are other ways of doing these embellishments of trees, including the ggtree package.
Can we vary the text size along with node size in R-igraph?
If yes, what attribute we can use? Any example?
(By text I mean the node Name)
For example I have plotted above network using igraph function as follows:
plot.igraph(net,vertex.label=V(net)$name,layout=layout.fruchterman.reingold,
edge.color="black",edge.width=Eweight,edge.curved=F)
If we look at label corresponding to each node, each has same size. I want to vary this label size according to their corresponding Node size. e.g. size("w1") > size("w5") > size("w6") and so on.
You can create reproducible example using a data.frame
library(igraph)
dat <- data.frame(name=c("Alice", "Bob", "Cecil"),age=c(48,33,45))
g<-graph.data.frame(dat)
Then change the change the some attributes
V(g)$label.cex <- seq(0.5,5,length.out=6) ## text size
V(g)$size <- seq(10,60,length.out=6) ## circle size proportional to text size
final plot
plot(g, vertex.label = V(g)$name,
vertex.shape="circle",
vertex.color="red"
)