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Questions tagged [upsetplot]

42 questions
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How do I add an axis break in Complexheatmap's upset plot?

I am making an upset plot using the ComplexHeatmap package (https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#upset-making-the-plot). Some of my bars are an order of magnitude higher than the rest. I would like to add a break…
ktm
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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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Label overlap in upset plot

I found the below Upset plot code here. The Orthogroups.GeneCount.tsv can be found here import pandas as pd from upsetplot import UpSet from upsetplot import from_memberships from matplotlib import pyplot as…
user3523406
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Error creating upset plot - ggupset producing redundant bars

I have a gene list like gene Sample PRKG1 D6 ERC2 D6 LINC01695 D6 CNTN5 D6 AC004704.1 D10 ERC2 D10 which I converted into a tibble using df %>% group_by(gene) %>% summarize(ID = list(Sample)) gene ID …
trisha
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R ggplot ggupset - Create inset with combinations that have fewer intersection

I am looking for a way to subset my input data so I can make a second upsetR plot that shows the resolution of the sample intersections that are <<100 (for example). As an example, I'm using the tidy_movies data from tidyverse and the ggupset…
shu251
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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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ModuleNotFoundError after installing PyUpSet

Reference: https://github.com/ImSoErgodic/py-upset Hello! I have installed pyupset via both pip, pip3, and the source directly, as described in the link above. The terminal is saying that I have it completely downloaded. However, when I go to spyder…
sdoctor
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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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python upset plot data type unclear

I am trying to make an upset plot using gene-disease association lists. I assume that I simply do not understand which data type is required as an input as most examples use artificially created datasets that are of the data type "int64". Upsetplot:…
Julia S
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Subsetting columns and counting the 1's (TURF analysis?)

The aim is to count the corresponding 1's in the rows of each subset (>2) of columns: 0 2 4 0 0 1 0 1 1 1 1 2 1 0 0 3 1 1 0 4 1 0 0 ... ... ... ... In above example we would have 4 subsets. Then the idea is to…
Sean_TBI_Research
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