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Questions tagged [upsetplot]

42 questions
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How to use upsetplot python for finding intersection in pandas dataframe

I'm trying to use upsetplot for finding the intersection between column data in a dataframe. I am using a code from the one provided by the developers of this library, like the following: import upsetplot from upsetplot import from_indicators, plot…
lavoisier_hosea
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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
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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
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How to install UpSetPlot on google colab

I am using google colab for python programming. however, the package UpSetPlot was not installed. I tried using the command: !pip install UpSetPlot but the following error appears: Collecting UpSetPlot Using cached…
s.abbaasi
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set analysis: create pandas series with intersections as index and values as counts

I've tried and tried, all day to try and make this work and it's starting to make me angry! All I want to do is create a necessary pandas series for input into upsetplot as detailed here: https://pypi.org/project/upsetplot/ I don't understand how…
Jeff S.
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How to sort the combination matrix of an UpSet plot by sets

I'm plotting some data from a list of named vectors using fromList() with the UpSetR package. But I need to sort the combination matrix by sets, just like an example on the ggupset GitHub page where from left to right you have first the sets with…
Hidroxiapatito
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UpsetR How to fix: Image being cut off when trying to export

I am using the UpsetR package to create a chart showing overlaps between different populations. However, when the plot is created it cuts off the numbers on the left-hand side bars and a bit of the set size title, I have tried adjusting the text…
Fortjos
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Error in start_col:end_col : argument of length 0 - UpSetR

I have a dataset like this: df <- structure(list(id = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40), a = c(0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1,…
user19745561
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How do I add multiple data points in a data set for Upset plot using R studio?

I am trying to create an Upset plot for 4 clinical data sets from 200 patients in R studio. I am only able to do so if I create a data frame and type each data point (0 or 1). Since I have 200 entries, it is difficult to type in for 4 clinical…
Tina Damodar
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How to change the labelling of the intersection size and set size?

How can I display the intersection size as percentage of total rows? How can I change the set size as percentage of total rows? The set size should display the marginals, i.e., the total TRUEs returned by one member (column)? { library(ggplot2) …
Sean_TBI_Research
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Obtaining a HashMap or dictionary and a diagram in Python to visualize the overlaps between multiple lists

Context: I roughly have a dictionary of about 130 lists in the form of a key and a list of indexes. {‘key1’:[0,1,2], ‘key2’: [2, 3, 4], ‘key3’:[5, 6],…, ‘key130’:[0, 450, 1103, 500,…]} Lists are all different sizes. This is a two-part problem…
Dianna Li
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How to make the Set size sidebars in Complex Upset the total number of items and the single "intersection" top bar the items only in that set?

When, sing the Complex Upset in R, if mode="inclusive_intersection" is chosen (which I need to show) the set size bars end up being the same as the single bars in the intersection size. I expected the side bars to be all the items in that group…
Panchito
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ggupset manually order intersections using R

I'm trying to make a ggupset plot, with a violin plot and intersections manually ordered. I would like to order the intersections (x axis or gene combinations) in the following order: Gene_A, Gene_B, Gene_D, Gene_E Gene_D with Gene_H, Gene_C with…
annieapple
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Change the size of the y axis in the matrix of. Complex Upset Plot R

How does now change the size of the labels (tick labels) of the y axis in the matrix section of an Upset plot made with Complex Upset in R? I tried using the matrix=(intersection_matrix()+theme(axis.title.y=element_text(size=200))) and nothing…
Panchito
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How to change labels in the Intersection Matrix in Complex Upset R?

I'm using ComplexUpset in R and I would like to know if changing the labels of the intersection matrix is possible. I attempted using upset( themes=upset_modify_themes( list( 'intersections_matrix'=scale_x_discrete("A"="label A",…
Panchito
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