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Questions tagged [upsetr]

58 questions
8
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3 answers

Stacked barplot in UpSetR

I have been looking for a way of having a stacked bar plot in an upsetR graph. I downloaded the movies data set (from here) and added a column having only two values "M" and "C". Below, information on how I loaded the data and added the "x"…
efrem
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8
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1 answer

Use a color palette for matrix points in UpSetR

Below I've constructed an Upset plot. I'm using a palette of colors to define the bar colors. Is there a way to do this for the matrix of connected dots as well? library(dplyr) library(RColorBrewer) library(UpSetR) movies <-…
Megatron
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6
votes
3 answers

Extract intersection list from upset object

I'm making some comparisons with UpSetR, and I'd like to save the lists of elements that fall into each intersection. Is this possible? I can't find it anywhere... It would be pretty tedious to do it manually (many lists), and since they're…
Matteo
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6
votes
5 answers

How to create a vector from elements in common in vectors R

I have several character vectors of genes containing names of the species in which they're found, and I made an UpSetR plot to show the number of species in common across genes. Now I'd like to do the opposite: Plotting the number of genes in common…
Guillermo Reales
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3
votes
1 answer

Problem with upset plot intersection numbers

I have four sets A, B, C and D like below: A <- c("ENSG00000103472", "ENSG00000130600", "ENSG00000177335", "ENSG00000177337", "ENSG00000178977", "ENSG00000180139", "ENSG00000180539", "ENSG00000187621", "ENSG00000188511", "ENSG00000197099",…
beginner
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3
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2 answers

UpsetR change set name labels in graph

I am trying to change the set name labels in my UpsetR plot (using Upset function) to be a string of multiple words. Instead of 'A', 'B', 'C' as the set labels I want to have the set labels appear as 'A Description', 'B Description', 'C…
PharmGirl
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3
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2 answers

In UpSetR, how to show decimal number on the intersection bar

I am making an upset diagram for the following data in percentages. This is a dummy example for my more complicated data. x <- c(a=80, b=9.9, c=5, 'a&b'=0.1, 'a&c'=1.65, 'c&b'=3.35) upset(fromExpression(x), order.by = "freq") I want these…
XtrimA
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2
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0 answers

How to adjust y-axis title position of UpSet plot in R?

I can't figure out how to adjust the position of the y-axis title in this UpSet plot. It is moved far over to the left due to the length of the variable names. I have created a replicable example below: library(UpSetR) library(dplyr) movies <-…
icedcoffee
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2
votes
1 answer

UpSetR sets.bar interacting different color and its sets intersections

hello I am creating upsetr plot not able figure out how can I plot the data as show in below image I saw different plot making similar to this but not same, Can any one suggest me an easy way to do it and seen some of the threads not able reproduce…
Shrilaxmi M S
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2
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1 answer

ComplexUpset: How can I plot ONLY specific intersections?

I am trying to make an upset plot that only shows specific intersections. I have 6 different fjords which generate too many intersections. I am only interested in plotting some of those: I have run this next script: upset(fjords, fjordnames,…
Sandra
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2
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2 answers

UpSetR group by color set

I've stared at this for a couple of hours and don't seem to have found a solution. I would like upSet diagram to be colored by set. For example, library('UpSetR') movies <- read.csv( system.file("extdata", "movies.csv", package = "UpSetR"), …
Gnils
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2
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0 answers

UpSetR with tranposed data frame in R

I have the following table mytable.tsv: ABCI15.1 IM3 ABCK16.1 IMNCY ABCK16.1 IM5 ABCI15.1 IM200/IM605 ABCM13.1 IM4 ABCN06.1 IM1182 ABCN20.1 IM21 ABCN06.1 IMNCY ABCP20.1 IM4 ABCM13.1 IM630 And I would like to make an…
Saraha
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2
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0 answers

How to make an UpSet plot in R with a transparent background?

Is it possible to make an UpSet plot with a transparent background? I have checked the documentation and there are no arguments related to the background colour. I have also tried saving directly as a .pdf but only a small section of the plot…
Mooholl
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2
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1 answer

upset plot with set size bars in right side

The UpSetR R package offers a wonderful method to upgrade the traditional Venn-diagram when multiple components/sets are to be compared. However, the upset plot in R (using UpSetR package) plots the set size (horizontal bars) on the left side of the…
Alemu Assefa
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2
votes
1 answer

UpsetR: add numeric labels to set size on plot

Is there any way to add labels on top of the set size bars in UpsetR similar to the show.numbers for the main intersection graph? test <- upset(grouped_hot, sets = c("A", "B", "C", "N"), nintersects …
PharmGirl
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