Questions tagged [upsetplot]
42 questions
3
votes
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
- 57
- 11
3
votes
3 answers
UpSetPlot from actual sets
I want to use the UpSetPlot given the actual sets I have, but I cannot find any example to use it this way. The standard example is this:
from upsetplot import generate_counts, plot
example = generate_counts()
plot(example,…
user5054
- 1,056
- 1
- 7
- 22
2
votes
1 answer
Rotate annotation in Upset plot of complex heatmap package
I want to show the numbers of the bars in the top annotation barplot in the Upset plot of ComplexHeatmap. However, I could only find parameters to rotate the name of the annotations, but not the annotations themselfes.
Taken from the ComplexHeatmap…
nebroth
- 132
- 1
- 7
2
votes
1 answer
How can I add a title and change other plot aesthetics for an UpSet plot in python?
I have installed and imported the following (using Google Colab):
!pip install upsetplot
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import upsetplot
from upsetplot import generate_data, plot
from upsetplot import…
code_to_joy
- 569
- 1
- 9
- 27
2
votes
0 answers
Combine scale_x_upset with scale_y_break
I made an upset plot using the ggupset package and added a break to the y axis with scale_y_break from the ggbreakpackage.
However, when I add scale_y_break, the combination matrix under the bar plot disappears.
Is there a way to combine the…
erikagucci
- 21
- 1
2
votes
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
- 673
- 4
- 13
2
votes
1 answer
Changing the figsize in the upsetplot module
How I can change the figsize in the upsetplot module in Python? I see that there is a fig parameter, but I don't get how to assign a new figure with a predefined size to it.
Elena_Kosourova
- 71
- 6
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
- 8
- 26
1
vote
1 answer
Colouring of the main bars in upset plot
I have a dataset consisting of 7 columns with values of 0 and 1 in r. The data has been defined at the last column into different groups based on the value. I want to colour the bars as per my group.I have 17 different combinations but I don't want…
user142632
- 41
- 4
1
vote
1 answer
How to display intersection values instead of distinct values in Upset plot
I tried to create an upset plot and display intersection among different sets.
But my upset plot is displaying dinstinct value counts among sets.
How do I change it to intersections instead of distinct counts?
This is my code:
mammals = ['Cat',…
Yash
- 275
- 1
- 8
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
- 4
- 20
1
vote
1 answer
How to show all sets in ggupset?
Is there a way to show unobserved sets in ggupset?
Reprex
In this example, I would like to show B even though it is not observed.
library(ggplot2)
library(ggupset)
df <- data.frame(x = I(list(c("A", "C"),
"A",
…
LMc
- 12,577
- 3
- 31
- 43
1
vote
1 answer
Python UpSetPlot returning error: 'RangeIndex' object has no attribute 'levels'
I have been trying to get an UpSetPlot to work and have not been having much luck.
My code is quite simple, I have already shaped the data in a CSV. Below is what I have been trying to run.
import pandas as pd
from matplotlib import pyplot as…
afroduck
- 143
- 8
1
vote
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
- 11
- 1
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