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Questions tagged [complex-upset]

Questions about ComplexUpset package usage.

14 questions
3
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1 answer

Upset plot python list row names

The upset plot tutorials on the documentation have this example with movies: https://upsetplot.readthedocs.io/en/stable/formats.html#When-category-membership-is-indicated-in-DataFrame-columns I wanted to know, after creating data from memberships…
Uqhah
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2
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1 answer

Complex Upset in R: Sort ascending by degree and descending within degree groups?

Following the method outlined here, the following code produces a complex upset plot where bars are colored by degree groups (e.g., number of combinations): library(tidyverse) library(ComplexUpset) movies =…
acircleda
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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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1 answer

How to to assign logarithmic scale to “Intersection size” using ComplexUpset library?

When I assigning a logarithmic scale to “Intersection size” using ComplexUpset library the bars disappear. Is there a way around?
Igal Seagal
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1
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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
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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
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0
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1 answer

Determination of the intersection size members in ComplexUpset by using R

I created a ComplexUpset plot. Then, I tried to obtain the members of the intersection which were illustrated in the "intersection size" part of the plot. For this purpose, I tried several ways but always, I got errors or the new datasets were…
Hasan Can Demirci
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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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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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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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1 answer

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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ComplexUpset R. How to add an annotation that uses another set of related data on a upset plot?

I'm using ComplexUpset in R. I have a results from a Transcription Experiment. It has 4 comparisons. Each gene in in each comparison can be significantly regulated. Furthermore, each can be positively regulated or negatively regulated or…
Panchito
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0
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Error in upset_data : unused argument (nsets = 5) What could be causing this and how coul I fix the issue?

I am very new to R and I would like to make UpSet plot of peptides. I have five lists (sets) in .txt format (ID_list_vysledok_pos_vs_healthy_files.txt, ID_list_vysledok_pos_neg_files.txt, ID_list_vysledok_New_vs_Old_collumn_files.txt,…
adam urminský
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0
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Memory management in R ComplexUpset Package

I'm trying to plot an stacked barplot inside an upset-plot using the ComplexUpset package. The plot I'd like to get looks something like this (where mpaa would be component in my example): I have a dataframe of size 57244 by 21, where one column is…
mrbelyash
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