UpSetR | R implementation of the UpSet set visualization technique | Data Visualization library

by hms-dbmi R Version: v1.4.0 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | UpSetR Summary

UpSetR is a R library typically used in Analytics, Data Visualization, D3 applications. UpSetR has no bugs, it has no vulnerabilities and it has low support. However UpSetR has a Non-SPDX License. You can download it from GitHub.

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

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Support

UpSetR has a low active ecosystem.

It has 678 star(s) with 140 fork(s). There are 38 watchers for this library.

It had no major release in the last 12 months.

There are 112 open issues and 107 have been closed. On average issues are closed in 531 days. There are 15 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of UpSetR is v1.4.0

Quality

UpSetR has 0 bugs and 0 code smells.

Security

UpSetR has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

UpSetR code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

UpSetR has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

UpSetR releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 1500 lines of code, 0 functions and 8 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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UpSetR Key Features

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UpSetR Examples and Code Snippets

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Community Discussions

Trending Discussions on UpSetR

Changing set name labels

Memory management in R ComplexUpset Package

Manual coloring of dots by set color in Complex Upset

UpSetR sets.bar interacting different color and its sets intersections

Manually order intersections UpSetR

Problem with upset plot intersection numbers

Venn Diagrams with `venneuler` in `R`: delete the name of the set from the plot and add elements name

Extract intersection list from upset object

How to plot binary data and colour presence by group in R

How to use custom font family in UpsetR plots?

QUESTION

Changing set name labels

Asked 2022-Feb-23 at 17:06

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?

...

ANSWER

Answered 2022-Feb-23 at 17:06

Generally "non-standard" column names should be avoided, but this might be an exception. You can use spaces and other special characters in column names if you quote them or surround them in backticks (and make sure they don't get autocorrected).

A couple options:

Source https://stackoverflow.com/questions/71239429

QUESTION

Memory management in R ComplexUpset Package

Asked 2021-Nov-24 at 13:47

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 ID and the other is type of recording, and other 19 columns are components from 1 to 19:

...

ANSWER

Answered 2021-Nov-24 at 13:47

Somehow, it works if you:

Tweak the min_size parameter so that the plot is not overloaded and makes a better impression
Making the first argument of ComplexUpset a sample with some data also helps, even if your sample is the whole dataset.

Source https://stackoverflow.com/questions/69974424

QUESTION

Manual coloring of dots by set color in Complex Upset

Asked 2021-Sep-22 at 15:39

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:

...

ANSWER

Answered 2021-Sep-22 at 15:37

The dots don't change color because you are passing fill (not color) to upset_query; you can keep using fill if you like but in that case you need to also change the shape of the dot so that they have area to be filled, which can be done using shape='circle filled' (there are other shapes too!).

Similarly, the scale_color_manual would not be a perfect choice in plain ggplot2, but given that it is overridden by ComplexUpset it is actually a good idea, but you will need to customize override.aes to make it display as intended.

Source https://stackoverflow.com/questions/69280909

QUESTION

UpSetR sets.bar interacting different color and its sets intersections

Asked 2021-Jun-07 at 10:30

hello I am creating upsetr plot not able figure out how can I plot the data as show in below image

I saw different plot making similar to this but not same, Can any one suggest me an easy way to do it and seen some of the threads not able reproduce few according my above image kind output

UpSetR group by color set

Use a color palette for matrix points in UpSetR

blog post

Thank you

...

ANSWER

Answered 2021-Jun-07 at 10:30

You can reproduce this plot using ComplexUpset 1.3 or newer.

Prepare the dataset:

Source https://stackoverflow.com/questions/67094573

QUESTION

Manually order intersections UpSetR

Asked 2021-Mar-29 at 14:24

I'm trying to manually order my intersections with UpSetR but I don't know if it's possible to do it. order.by only allows freq or degree and I don't see any other parameter that could produce what I want.

...

ANSWER

Answered 2021-Mar-29 at 10:17

I just found the solution with ComplexUpset package :

Source https://stackoverflow.com/questions/66851857

QUESTION

Problem with upset plot intersection numbers

Asked 2021-Feb-23 at 12:28

I have four sets A, B, C and D like below:

...

ANSWER

Answered 2021-Feb-23 at 12:28

The numbers are correct! The issue is very specific and complex.

There are different ways to calculate set intersection size:

"distinct" mode
"intersect" mode
"union" mode

UpSetR uses the "distinct" mode.

The "intersect" mode may be what the user expects.

ComplexHeatmap and ComplexUpset packages allows the user to choose which mode to use.

I found a real sufficient explanation by Jakob Rosenthal here https://github.com/hms-dbmi/UpSetR/issues/72 especially this graphic:

Source https://stackoverflow.com/questions/66323268

QUESTION

Venn Diagrams with `venneuler` in `R`: delete the name of the set from the plot and add elements name

Asked 2021-Feb-03 at 16:46

For the past few days I have been trying to figure out how to draw a Venn diagram from an arbitrary number of sets and came across the R package venneuler. This code:

...

ANSWER

Answered 2021-Feb-03 at 16:46

You could directly modify v$labels:

Source https://stackoverflow.com/questions/65994218

QUESTION

Extract intersection list from upset object

Asked 2020-Nov-26 at 21:48

I'm making some comparisons with UpSetR, and I'd like to save the lists of elements that fall into each intersection. Is this possible? I can't find it anywhere...

It would be pretty tedious to do it manually (many lists), and since they're calculated anyway not being able to save them is frustrating

...

ANSWER

Answered 2020-Nov-26 at 21:48

There is no ready upSetR function for this (yet). But, it is possible to extract it:

Source https://stackoverflow.com/questions/65027133

QUESTION

How to plot binary data and colour presence by group in R

Asked 2020-Jul-13 at 13:41

I'm an R beginner and I'm trying to plot simple presence/absence binary data. I have searched everywhere but I can't work out if it's possible to colour the plot by grouping/metadata. So far I have a simple plot with ggplot with the following code:

my data looks like this:

...

ANSWER

Answered 2020-Jul-13 at 13:41

You can do all this in ggplot2, with a little help from reshape2 to get your data into long format. Here, I have assumed you have a data frame called data that looks like your second data image. I had to put your image through OCR to recreate your data since you didn't make a reproducible example, so it may not be totally accurate:

Source https://stackoverflow.com/questions/62876384

QUESTION

How to use custom font family in UpsetR plots?

Asked 2020-Mar-13 at 00:50

I am trying to create set plot using the UpSetR package; however, I'd like to control the family of fonts. The ideal approach would be using theme function from ggplot2 but this is not supported at the moment by UpSetR (there's an open issue from 2016 on GitHub here) and results in NULL.

Example to create test plot: ...

ANSWER

Answered 2020-Mar-13 at 00:50

One way of achieving this with another UpSet implementation would be:

Source https://stackoverflow.com/questions/60189966

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install UpSetR

Install the latest released version from CRAN. Download the latest development code of UpSetR from GitHub using devtools with.

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