Questions tagged [upsetr]
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upsetr
50
questions
0
votes
1
answer
247
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How to set y-axis title and change the font style in UpsetR plot?
I am trying to plot an intersection graph using UpSetR for an Orthogroup gene count dataset that looks like this -
I need to highlight certain intersections, the names 'Mdong', 'Mfastidious' etc, ...
- 33
2
votes
1
answer
525
views
How to remove the set size plot and add percentage with the numbers on the top of the bars
I am trying to move away from the Venn plots for anything more than 3 conditions/samples in my experiments. It just become more and more difficult to interpret.
UpSet plots using UpSetR::upset() work ...
- 1,056
1
vote
0
answers
271
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Changing the y-axis scale for intersection_size from ComplexUpset package
I have created 4 different upset plots using the ComplexUpset package in R. The 4 plots have different intersection sizes since the length of the data frames range from 300 to 12000. Since, I want to ...
- 11
1
vote
1
answer
208
views
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, ...
- 822
0
votes
1
answer
205
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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 ...
3
votes
2
answers
1k
views
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,...
- 780
0
votes
1
answer
913
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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, ...
- 145
0
votes
1
answer
100
views
How to edit package functions in R?
I would like to make subtle changes to a visualisation from the UpSetR package. Within the upset() function there is another sub-function called Make_size_plot() that creates the bar chart which I ...
- 27
0
votes
0
answers
65
views
Combination analysis help in R
Essentially, I have a dataframe of 300 patients each with 25 recorded variables. I am trying to work out the most common combinations of these variables using the UpsetR package which worked fine for ...
0
votes
0
answers
516
views
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 ...
1
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0
answers
517
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Manually order the set fails in UpsetR
I have tried to use UpsetR to visualise the input file, which can be found here. How is it possible to make UpsetR accept an order defined in sets?
with keep.order = T
with keep.order = F
> ...
- 523
1
vote
1
answer
270
views
UpSetR error when using queries: replacement has 1 row, data has 0
I have tried to use UpsetR to visualize the input file which can be found here
> library("UpSetR")
> orthogroups_df<- read.table("orthogroups.GeneCount.tsv", header=T, ...
- 523
1
vote
1
answer
392
views
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 ...
- 251
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0
answers
100
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Is there a R function to add the count of horizontal bars beside the bars in UpSetR plot?
I used the upset(fromList(x), show.numbers = 'yes', order.by = 'freq') query to plot the UpSetR plot. But it is showing only the count of vertical bars on the top of vertical bars. I want the count ...
- 13
0
votes
1
answer
663
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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, ...
