Random network plot setting in R - r

I generated a random network by using 620 nodes and 2102 edges. I want to visualize it by using plot.But, 1. not sure how to make the plot nicer (make nodes more separated at least)? 2.adjust the node size based on 'degree'.
my codes are:
set.seed(42)
Network_random <- erdos.renyi.game(620,2102,type='gnm')
plot(Network_random, vertex.col="degree", main="Network Random",layout=layout_nicely,margin=-0.25)
my current plot is as below:

What about this?
set.seed(42)
Network_random <- erdos.renyi.game(620, 2102, type = "gnm") %>%
set_vertex_attr(name = "size", value = pmax(degree(.), 5)) %>%
plot(vertex.label = NA, vertex.color = degree(.), main = "Network Random", margin = -0.25)

Related

R (networkD3) Sankey Diagram left AND right sinking?

I am trying to produce a Sankey diagram with the help of this page:
https://www.r-graph-gallery.com/321-introduction-to-interactive-sankey-diagram-2.html
Now, I modified the data a bit, and was wondering if I can right and left-sink the nodes, i.e. that the top-nodes are always to the left (aligned) and the last nodes always to the right. It appears that networkd3 only has the sinkright option.
Using the following code:
library(networkD3)
library(dplyr)
# A connection data frame is a list of flows with intensity for each flow
links <- data.frame(
source=c("group_A", "group_B", "group_C", "group_C"),
target=c("group_D", "group_C", "group_F", "group_G"),
value=c(3, 4, 3, 1)
)
# From these flows we need to create a node data frame: it lists every entities involved in the flow
nodes <- data.frame(
name=c(as.character(links$source),
as.character(links$target)) %>% unique()
)
# With networkD3, connection must be provided using id, not using real name like in the links dataframe.. So we need to reformat it.
links$IDsource <- match(links$source, nodes$name)-1
links$IDtarget <- match(links$target, nodes$name)-1
# Make the Network
p <- sankeyNetwork(Links = links, Nodes = nodes,
Source = "IDsource", Target = "IDtarget",
Value = "value", NodeID = "name",
fontSize=20)
p
Gives me this output:
Sankey Plot
It looks already promising, but I would like to move group_A to the left side (while keeping the right side aligned). Is this possible?
It appears this seems to be not possible with networkD3 out of the box. However, I found out that plotly offers a x position option, which worked in the end:
fig <- plot_ly(
type = "sankey",
arrangement = "snap",
node = list(
label = nodes$name,
x = c(0.1, 0.1, 0.5, 0.7, 0.7, 0.7),
pad = 10), # 10 Pixel
link = list(
source = links$IDsource,
target = links$IDtarget,
value = links$value))
fig <- fig %>% layout(title = "Sankey with manually positioned node")
fig

How to programmatically determine the column indices of principal components using FactoMineR package?

Given a data frame containing mixed variables (i.e. both categorical and continuous) like,
digits = 0:9
# set seed for reproducibility
set.seed(17)
# function to create random string
createRandString <- function(n = 5000) {
a <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE))
paste0(a, sprintf("%04d", sample(9999, n, TRUE)), sample(LETTERS, n, TRUE))
}
df <- data.frame(ID=c(1:10), name=sample(letters[1:10]),
studLoc=sample(createRandString(10)),
finalmark=sample(c(0:100),10),
subj1mark=sample(c(0:100),10),subj2mark=sample(c(0:100),10)
)
I perform unsupervised feature selection using the package FactoMineR
df.princomp <- FactoMineR::FAMD(df, graph = FALSE)
The variable df.princomp is a list.
Thereafter, to visualize the principal components I use
fviz_screeplot() and fviz_contrib() like,
#library(factoextra)
factoextra::fviz_screeplot(df.princomp, addlabels = TRUE,
barfill = "gray", barcolor = "black",
ylim = c(0, 50), xlab = "Principal Component",
ylab = "Percentage of explained variance",
main = "Principal Component (PC) for mixed variables")
factoextra::fviz_contrib(df.princomp, choice = "var",
axes = 1, top = 10, sort.val = c("desc"))
which gives the following Fig1
and Fig2
Explanation of Fig1: The Fig1 is a scree plot. A Scree Plot is a simple line segment plot that shows the fraction of total variance in the data as explained or represented by each Principal Component (PC). So we can see the first three PCs collectively are responsible for 43.8% of total variance. The question now naturally arises, "What are these variables?". This I have shown in Fig2.
Explanation of Fig2: This figure visualizes the contribution of rows/columns from the results of Principal Component Analysis (PCA). From here I can see the variables, name, studLoc and finalMark are the most important variables that can be used for further analysis.
Further Analysis- where I'm stuck at: To derive the contribution of the aforementioned variables name, studLoc, finalMark. I use the principal component variable df.princomp (see above) like df.princomp$quanti.var$contrib[,4]and df.princomp$quali.var$contrib[,2:3].
I've to manually specify the column indices [,2:3] and [,4].
What I want: I want to know how to do dynamic column index assignment, such that I do not have to manually code the column index [,2:3] in the list df.princomp?
I've already looked at the following similar questions 1, 2, 3 and 4 but cannot find my solution? Any help or suggestions to solve this problem will be helpful.
Not sure if my interpretation of your question is correct, apologies if not. From what I gather you are using PCA as an initial tool to show you what variables are the most important in explaining the dataset. You then want to go back to your original data, select these variables quickly without manual coding each time, and use them for some other analysis.
If this is correct then I have saved the data from the contribution plot, filtered out the variables that have the greatest contribution, and used that result to create a new data frame with these variables alone.
digits = 0:9
# set seed for reproducibility
set.seed(17)
# function to create random string
createRandString <- function(n = 5000) {
a <- do.call(paste0, replicate(5, sample(LETTERS, n, TRUE), FALSE))
paste0(a, sprintf("%04d", sample(9999, n, TRUE)), sample(LETTERS, n, TRUE))
}
df <- data.frame(ID=c(1:10), name=sample(letters[1:10]),
studLoc=sample(createRandString(10)),
finalmark=sample(c(0:100),10),
subj1mark=sample(c(0:100),10),subj2mark=sample(c(0:100),10)
)
df.princomp <- FactoMineR::FAMD(df, graph = FALSE)
factoextra::fviz_screeplot(df.princomp, addlabels = TRUE,
barfill = "gray", barcolor = "black",
ylim = c(0, 50), xlab = "Principal Component",
ylab = "Percentage of explained variance",
main = "Principal Component (PC) for mixed variables")
#find the top contributing variables to the overall variation in the dataset
#here I am choosing the top 10 variables (although we only have 6 in our df).
#note you can specify which axes you want to look at with axes=, you can even do axes=c(1,2)
f<-factoextra::fviz_contrib(df.princomp, choice = "var",
axes = c(1), top = 10, sort.val = c("desc"))
#save data from contribution plot
dat<-f$data
#filter out ID's that are higher than, say, 20
r<-rownames(dat[dat$contrib>20,])
#extract these from your original data frame into a new data frame for further analysis
new<-df[r]
new
#finalmark name studLoc
#1 53 b POTYQ0002N
#2 73 i LWMTW1195I
#3 95 d VTUGO1685F
#4 39 f YCGGS5755N
#5 97 c GOSWE3283C
#6 58 g APBQD6181U
#7 67 a VUJOG1460V
#8 64 h YXOGP1897F
#9 15 j NFUOB6042V
#10 81 e QYTHG0783G
Based on your comment, where you said you wanted to 'Find variables with value greater than 5 in Dim.1 AND Dim.2 and save these variables to a new data frame', I would do this:
#top contributors to both Dim 1 and 2
f<-factoextra::fviz_contrib(df.princomp, choice = "var",
axes = c(1,2), top = 10, sort.val = c("desc"))
#save data from contribution plot
dat<-f$data
#filter out ID's that are higher than 5
r<-rownames(dat[dat$contrib>5,])
#extract these from your original data frame into a new data frame for further analysis
new<-df[r]
new
(This keeps all the original variables in our new data frame since they all contributed more than 5% to the total variance)
There are a lot of ways to extract contributions of individual variables to PCs. For numeric input, one can run a PCA with prcomp and look at $rotation (I spoke to soon and forgot you've got factors here so prcomp won't work directly). Since you are using factoextra::fviz_contrib, it makes sense to check how that function extracts this information under the hood. Key factoextra::fviz_contrib and read the function:
> factoextra::fviz_contrib
function (X, choice = c("row", "col", "var", "ind", "quanti.var",
"quali.var", "group", "partial.axes"), axes = 1, fill = "steelblue",
color = "steelblue", sort.val = c("desc", "asc", "none"),
top = Inf, xtickslab.rt = 45, ggtheme = theme_minimal(),
...)
{
sort.val <- match.arg(sort.val)
choice = match.arg(choice)
title <- .build_title(choice[1], "Contribution", axes)
dd <- facto_summarize(X, element = choice, result = "contrib",
axes = axes)
contrib <- dd$contrib
names(contrib) <- rownames(dd)
theo_contrib <- 100/length(contrib)
if (length(axes) > 1) {
eig <- get_eigenvalue(X)[axes, 1]
theo_contrib <- sum(theo_contrib * eig)/sum(eig)
}
df <- data.frame(name = factor(names(contrib), levels = names(contrib)),
contrib = contrib)
if (choice == "quanti.var") {
df$Groups <- .get_quanti_var_groups(X)
if (missing(fill))
fill <- "Groups"
if (missing(color))
color <- "Groups"
}
p <- ggpubr::ggbarplot(df, x = "name", y = "contrib", fill = fill,
color = color, sort.val = sort.val, top = top, main = title,
xlab = FALSE, ylab = "Contributions (%)", xtickslab.rt = xtickslab.rt,
ggtheme = ggtheme, sort.by.groups = FALSE, ...) + geom_hline(yintercept = theo_contrib,
linetype = 2, color = "red")
p
}
<environment: namespace:factoextra>
So it's really just calling facto_summarize from the same package. By analogy you can do the same thing, simply call:
> dd <- factoextra::facto_summarize(df.princomp, element = "var", result = "contrib", axes = 1)
> dd
name contrib
ID ID 0.9924561
finalmark finalmark 21.4149175
subj1mark subj1mark 7.1874438
subj2mark subj2mark 16.6831560
name name 26.8610132
studLoc studLoc 26.8610132
And that's the table corresponding to your figure 2. For PC2 use axes = 2 and so on.
Regarding "how to programmatically determine the column indices of the PCs", I'm not 100% sure I understand what you want, but if you just want to say for column "finalmark", grab its contribution to PC3 you can do the following:
library(tidyverse)
# make a tidy table of all column names in the original df with their contributions to all PCs
contribution_df <- map_df(set_names(1:5), ~factoextra::facto_summarize(df.princomp, element = "var", result = "contrib", axes = .x), .id = "PC")
# get the contribution of column 'finalmark' by name
contribution_df %>%
filter(name == "finalmark")
# get the contribution of column 'finalmark' to PC3
contribution_df %>%
filter(name == "finalmark" & PC == 3)
# or, just the numeric value of contribution
filter(contribution_df, name == "finalmark" & PC == 3)$contrib
BTW I think ID in your example is treated as numeric instead of factor, but since it's just an example I'm not bothering with it.

Show edge attributes as label with igraph

I am using igraph in R for network analysis. I want to display an edge attribute on each line in the plot. An example is below
df <- data.frame(a = c(0,1,2,3,4),b = c(3,4,5,6,7))
nod <- data.frame(node = c(0:7),wt = c(1:8))
pg <- graph_from_data_frame(d = df, vertices = nod,directed = F)
plot(pg)
I want the value of the "wt" feature to show up between each node on the line, or preferably, in a little gap where the line breaks.
Is it possible to make this happen?
Use the parameter edge.label to assign labels of the edges, I used - probably wrong - nod$wt. Of course, you could assign other labels.
You could use the following code:
# load the package
library(igraph)
# your code
df <- data.frame(a = c(0,1,2,3,4),b = c(3,4,5,6,7))
nod <- data.frame(node = c(0:7),wt = c(1:8))
pg <- graph_from_data_frame(d = df, vertices = nod,directed = F)
# plot function with edge.label added
plot(pg, edge.label = nod$wt)
Please, let me know whether this is what you want.

How to take a sample from a large plot to show in knitr-PDF

I often create large plots in RStudio which I save to PDF but would also like to partly show in the PDF knitr report.
Is there a way to create the full object then cut a piece (ideally top left corner) and include that second picture in the PDF report?
as example, a pheatmap code that produces a plot with 56 cols and 100's of rows. I would like to show only the left-top-most 10col and 10 rows but if I sample the input data, I obviously get another plot due to the clustering being done on different data. Also, I would love a solution applicable to any plot types (not only pheatmap).
drows <- "euclidean"
dcols <- "euclidean"
clustmet <- "complete"
col.pal <- c("lightgrey","blue")
main.title <- paste("Variant (freq>", minfreq, "%) in all samples", sep="")
hm.parameters.maj <- list(hm.maj.data,
color = col.pal,
fontsize = 10,
cellwidth = 14,
cellheight = 14,
scale = "none",
treeheight_row = 200,
kmeans_k = NA,
show_rownames = T,
show_colnames = T,
main = main.title,
clustering_method = clustmet,
cluster_rows = TRUE,
cluster_cols = FALSE,
clustering_distance_rows = drows,
clustering_distance_cols = dcols,
legend=FALSE)
# To draw the heatmap on screen (comment-out if you run the script from terminal)
do.call("pheatmap", hm.parameters.maj)
# To draw to file (you may want to adapt the info(header(vcf))sizes)
outfile <- paste("major-variants_heatmap_(freq>", minfreq, ")_", drows, ".pdf", sep="")
do.call("pheatmap", c(hm.parameters.maj, filename=outfile, width=24, height=35))
Thanks in advance
Stephane

Stack bar generated by Phyloseq

I am using this R package called "phyloseq" to analyze the bioinformatic data.
otumat = matrix(sample(1:100, 100, replace = TRUE), nrow = 10, ncol = 10)
otumat
rownames(otumat) <- paste0("OTU", 1:nrow(otumat))
colnames(otumat) <- paste0("Sample", 1:ncol(otumat))
otumat
taxmat = matrix(sample(letters, 70, replace = TRUE), nrow = nrow(otumat), ncol = 7)
rownames(taxmat) <- rownames(otumat)
colnames(taxmat) <- c("Domain", "Phylum", "Class", "Order", "Family", "Genus",
"Species")
taxmat
library("phyloseq")
OTU = otu_table(otumat, taxa_are_rows = TRUE)
TAX = tax_table(taxmat)
OTU
TAX
physeq = phyloseq(OTU, TAX)
physeq
plot_bar(physeq, fill = "Family")
So the bar graph generated do not stack the same Family together. For example, there are two separate "I" blocks in sample 10. I know phyloseq plot graph using ggplot2. Does any one know what ggplot2 associated codes I can add to the lot_bar(physeq, fill = "Family") to stack the same family together in the bar graph?
You need to reorder the levels of the factor being used for the x-axis. physeq presumably has a column called "Sample" (don't have the relevant package installed), you need to reorder the levels in this.
It should be possible to use a command like this
physeq$Sample <- factor(physeq$Sample, levels = paste0("Sample", 1:10))
Then it should plot correctly.
You might need to dig to find the relevant part to change
Actually, with respect, the plot_bar function does already do what you're asking:
# preliminaries
rm(list = ls())
library("phyloseq"); packageVersion("phyloseq")
data("GlobalPatterns")
gp.ch = subset_taxa(GlobalPatterns, Phylum == "Chlamydiae")
# the function call that does what you're asking for
plot_bar(gp.ch, fill = "Family")
See the following help tutorial for more details, examples:
https://joey711.github.io/phyloseq/plot_bar-examples.html
You can also specify the x-axis grouping as well.

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