I am new to R.
I want to create a massive tree diagram that represent a Lotto game in R that looks like Tree Diagram 1 in this picture(I made it via PowerPoint):
The problem is I need to draw 6 balls out of 45 balls. The totally elements in this case will be 127. I tried to create a tree diagram using PowerPoint and it looks like Tree Diagram 2.
Then I gave up. I can't type "match' and "no match" and calculate the probability manually for such a massive diagram.
How can I create a tree diagram that looks like Tree Diagram 2 that has similar labels in Tree Diagram 1?
The DiagrammeR package should be helpful:
library(DiagrammeR)
nodes <- create_nodes(nodes = 1:7, type = "number")
edges <- create_edges(from = c(1, 1, 2, 2, 3, 3),
to = c(2, 3, 4, 5, 6, 7),
rel = "leading to")
graph <- create_graph(nodes_df = nodes,
edges_df = edges,
graph_attrs = "layout = dot",
node_attrs = "fontname = Helvetica",
edge_attrs = "color = gray20")
# View the graph
render_graph(graph)
You can get "fancy" with the programming and labels accordingly:
nodes <- create_nodes(nodes = 1:7, type = "number",
label = c("Lotto", rep(c("match", "no match"), times = 3)))
### Same Code as Above...
Related
I am trying to make a panel plots of 3 sankey diagram in R using networkD3 library. The Sankey diagrams are well generated and I have assigned three variables (p1, p2 and p3) to the plots. Now I want to combine them using ggarrange into one single plot using the code below;
ggarrange(p1, p2, p3, labels = c("A", "B", "C"), ncol = 1, nrow = 3)
But, I keep getting the following error.
Warning message:
In as_grob.default(plot) :
Cannot convert object of class sankeyNetworkhtmlwidget into a grob.
Apparently, ggarrange does not accept the format of my plots. How can I convert them into a format that ggarange will accept.
Here is the code that I used to generate the final Sankey Diagram for the first one (p1). The rest two (p2, p3) are generated using the same code.
nodes = data.frame("name" = c("Rocket 1", "Kerosene","Carbon IV Oxide",
"Aluminium IV Oxide","Sulphur IV Oxide"))
links = as.data.frame(matrix(c(0, 1, 488.4, 1, 2, 576.7, 1, 3, 24.4,
1, 4, 0.3), byrow = TRUE, ncol = 3))
p1 = names(links) = c("source", "target", "value")
p1 = sankeyNetwork(Links = links, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
fontSize= 12, nodeWidth = 20)
I would really appreciate some help with this. Thank you.
I am building a large map where a number of observed variables map onto latent variables. When using DiagrammeR to generate the map, all the observed items (indicated by squares) appear in a single row. I was wondering if there was a way to sort them into multiple rows, say 5 or 10 in a row? The example below is based on actual data where there are 30+ items that map to one latent variable. The final map will have multiple sets of these, but right now, I am working on getting one to display correctly:
library(tidyverse)
library(DiagrammeR)
nodes <- create_node_df(
n=33,
nodes = 33,
label = make.unique(rep(letters, length.out = 33), sep=''),
tooltip = make.unique(rep(letters, length.out = 33), sep=''),
fontsize= 7,
shape = c("ellipse", "ellipse", rep("square", 31)),
fillcolor = "white",
width = 1,
height = 1,
)
# lines
edges <- create_edge_df(
from=c(1,rep(2,32)),
to = c(2,3,seq(3, 33, 1)),
)
create_graph(nodes_df = nodes,
edges_df = edges,
) %>%
render_graph(layout="tree")
This renders as:
However, what I am going for is more like:
I'm creating heatmaps in R using heatmap.2 (I think it needs to be heatmap.2 because I'm using 1 dataset to generate the colours of the heatmap and a second dataset to overlay numerical data).
Here is a sample of my code so far. The actual data set is 30 columns and 1000 rows.
heatmap_all_data <-
data.frame(name = c("John", "Mark", "Luke", "Jack", "Will", "Jim", "Clive", "Steve"),
trait_1 = c(1, 2, 5, 8, 5, 3, 7, 8),
trait_2 = c(5, 7, 3, 4, 6, 3, 2, 1)) %>%
column_to_rownames(var="name")
heatmap_colour <- colorRampPalette(brewer.pal(11, "RdYlBu"))(1000)
heatmap.2(as.matrix(heatmap_all_data),
scale = "column",
key = FALSE,
dendrogram = "none",
Rowv = FALSE,
Colv = FALSE,
trace = "none",
col = rev(heatmap_colour),
labRow = row.names(heatmap_all_data))
Which generates the following heatmap: https://i.stack.imgur.com/lK8Sc.png
NOW, the problem is I only want a subsection of this data, e.g I want the following heatmap:
heatmap_part_data <-
data.frame(name = c("John", "Mark", "Luke"),
trait_1 = c(1, 2, 5),
trait_2 = c(5, 7, 3)) %>%
column_to_rownames(var="name")
heatmap_colour <- colorRampPalette(brewer.pal(11, "RdYlBu"))(1000)
heatmap.2(as.matrix(heatmap_part_data),
scale = "column",
key = FALSE,
dendrogram = "none",
Rowv = FALSE,
Colv = FALSE,
trace = "none",
col = rev(heatmap_colour),
labRow = row.names(heatmap_part_data))
https://i.stack.imgur.com/j33Ic.png
BUT, I want each cell to keep the same colours as the original. I.e. I want the colours in my subsetted heatmap to be relative to the total data and not just the subsetted data. (In the real example I want to show 10 out of 1000 entries).
So, I need to either "zoom in" and rescale the top section of the heatmap and then crop the image, extract the top section of the heatmap into a new object while maintaining the same colours, or extract information about the colours in the full heatmap and overwrite the default colours in the subsetted heatmap.
The goal is basically to output an image of the subsetted data heatmap with each colour in each cell the same as in the all_data heatmap.
I hope this is clear - please advise if you need any clarification!
Many thanks for taking the time to read and I hope someone can help.
Best,
Ryan
Found the solution!
So I switched from heatmap.2 to heatmaply - same functionality but with interactivity. With heatmaply you can drag an area over the heatmap and zoom into that area which gives the desired result but I wanted to consistently zoom to a specific area.
From this website (https://plotly.com/r/axes/) I found out about the Layout function of the wider plotly library (that heatmaply is part of).
So to the existing code you can add:
%>% layout(yaxis = list(range = c(10.5, 0.5)))
(Need to add 0.5 to centre the rows properly)
Et voila! The heatmap colours are generated relative to the wider dataset but only a subset is shown.
This question already has an answer here:
(igraph) Grouped layout based on attribute
(1 answer)
Closed 2 years ago.
My example:
library(igraph)
links <- cbind.data.frame(from = rep("A", 6),
to = LETTERS[1:6],
weight = rep((1:3), each =2))
nodes <- cbind.data.frame(id = LETTERS[1:6],
feature = rep((1:3), each =2))
net <- graph_from_data_frame(d = links, vertices = nodes, directed = T)
V(net)$color <- V(net)$feature
plot(net, vertex.size=30, edge.arrow.size = 0)
The resulting figure looks like below:
What I want is to arrange the same colored node together, as shown in the following figure. The same colored nodes are next to each other.
I have found a very simple way to do it. Just need to use as_star layout
LO <- layout_(net, as_star())
plot(net, vertex.size = 30, edge.arrow.size = 0, layout = LO)
I want to create a flowchart with the R package DiagrammeR. The text of some of the nodes should have a line break.
Consider the following reproducible example in R:
library("DiagrammeR")
# Create a node data frame (ndf)
ndf <- create_node_df(n = 4,
label = c("hi stacko", "aaa", "bbb", "ccc"))
# Create an edge data frame (edf)
edf <- create_edge_df(from = c(1, 2, 3, 3),
to = c(4, 3, 1, 4))
# Create a graph with the ndf and edf
graph <- create_graph(nodes_df = ndf,
edges_df = edf)
# Create a PDF file for the graph (`graph.pdf`)
graph %>%
render_graph()
In this flowchart, I would like to add a line break between "hi" and "stacko" in the lower left node. I found some sources that suggested <br> or \n. Unfortunately, both did not work.
Question: How could I insert a line break in DiagrammeR?
This works for me:
ndf <- create_node_df(n = 4,label = c("hi\nstacko", "aaa", "bbb", "ccc"))
and, when run with the remainder of the code, produces the following diagram: