Questions tagged [upsetr]
58 questions
2
votes
1 answer
Using queries in UpSetR
I am trying to use the query capabilites in the package UpSetR to highlight certain items depending on one variable.
My dataset Dropbox link
I can do a basic plot without any problems:
stress <- read_delim("upset_plot_high_freq.csv", "\t",…
biojl
- 1,060
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1
vote
1 answer
Removing Isolated Variables in UpSetR Plot
This is my situation:
library(UpSetR)
movies <- read.csv(system.file("extdata", "movies.csv", package = "UpSetR"), header = TRUE, sep = ";")
upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thriller", "Romance", "War",…
Borexino
- 802
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1
vote
1 answer
Add labels to upset plot, so the values of intersection would be visible along the number of intersection
I have multiple character vectors containing gene names found in some analyzed samples (cells). I would like to compare those sets and figure out whether they have some genes in common (and if they do, I would like to know how many and which genes…
ramen
- 691
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1
vote
0 answers
Manually order the set fails in UpsetR
I have tried to use UpsetR to visualise the input file, which can be found here. How is it possible to make UpsetR accept an order defined in sets?
with keep.order = T
with keep.order = F
> library("UpSetR")
> orthogroups_df<-…
user3523406
- 309
- 2
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1
vote
1 answer
UpSetR error when using queries: replacement has 1 row, data has 0
I have tried to use UpsetR to visualize the input file which can be found here
> library("UpSetR")
> orthogroups_df<- read.table("orthogroups.GeneCount.tsv", header=T, stringsAsFactors = F)
> #All species
> selected_species <-…
user3523406
- 309
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- 17
1
vote
1 answer
Changing set name labels
I can see that this has been asked several times before, but I can no find a method that works. Are there any clever people out there that can figure this out?
data.frame(
fast_car = sample(0:1, 35, replace = TRUE),
slow_bus =…
William Hurt
- 37
- 6
1
vote
1 answer
Manual coloring of dots by set color in Complex Upset
I would like to create an UpSet plot using the ComplexUpset package. I would like to manually color the dots in the intersection matrix to match the sets' color.
Here's what I've attempted so far:
movies <- read.csv( system.file("extdata",…
moniker
- 37
- 5
1
vote
1 answer
Plot a histogram together with an UpSet plot in R
I have a data frame that looks like this,
df <- data.frame(type=c("SNP","DEL","SNP","SNP"),geneA=c(1,1,1,0), geneB=c(0,0,1,1), geneC=c(1,0,0,1))
type geneA geneB geneC
1 SNP 1 0 1
2 DEL 1 0 0
3 SNP 1 1 …
LDT
- 2,856
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1
vote
2 answers
Move axis title towards plot and keep combmatrix labels
I am trying to move the y axis title towards the ticks. However, I'm having trouble doing this without cutting off the combmatrix labels. I've tried both with ggupset and ggplot functions. See reprex below.
Thank you for your…
maia-sh
- 537
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1
vote
1 answer
Manually order intersections UpSetR
I'm trying to manually order my intersections with UpSetR but I don't know if it's possible to do it. order.by only allows freq or degree and I don't see any other parameter that could produce what I want.
a <- list(one = c(1, 2, 3, 5,11,19),
…
Basti
- 1,703
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1
vote
0 answers
individualizing the UpSetR or ComplexUpset (combining the intersections + queries + keep.order + group.by)
I would like to get a plot which on the left side keeps 6 rows in the order listed S1-6, and as for columns I'm only am interested in the selected intersections (only non-empty S1 and S2 and one specific empty S1-S2 intersect).
upset(df,
sets =…
Anna Cot
- 11
- 2
1
vote
1 answer
How to manually order the set size bar plot of UpsetR
I have the following code:
library(UpSetR)
listInput <- list(one = c(1, 2, 3, 5, 7, 8, 11, 12, 13),
two = c(1, 2, 4, 5, 10),
three = c(1, 5, 6, 7, 8, 9, 10, 12, 13))
upset(fromList(listInput))
which produces…
littleworth
- 4,781
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1
vote
1 answer
How to save upsetr graph as an image file from within function?
UpSetR graphs are not saving properly when I call f. What is being saved to tmp.tiff is a blank image file. If I debug into the function, then it saves properly.
f <- function(tmp){
tmp <- tmp %>%
fromList() %>%
upset()
tiff(filename =…
iich
- 145
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1
vote
1 answer
Trying to plot UpSetR and getting an error
I have a script that looks like this:
library("UpSetR")
Data<- read.table(file=file.choose(), header=T, fill = TRUE);
Data <- as.data.frame(Data);
head(Data);
GEO<- colnames(Data);
upset(Data, sets = GEO, nsets = 6);
Data looks like…
Genetics
- 279
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1
vote
1 answer
How to use custom font family in UpsetR plots?
I am trying to create set plot using the UpSetR package; however, I'd like to control the family of fonts. The ideal approach would be using theme function from ggplot2 but this is not supported at the moment by UpSetR (there's an open issue from…
gofraidh
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