ggcyto | Visualize Cytometry data with ggplot2 | Data Visualization library

by RGLab R Version: bioc_3.12 License: MIT

X-Ray Key Features Code Snippets(1)Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | ggcyto Summary

ggcyto is a R library typically used in Analytics, Data Visualization, D3 applications. ggcyto has no vulnerabilities, it has a Permissive License and it has low support. However ggcyto has 531 bugs. You can download it from GitHub.

ggcyto is a cytometry data visualization tool built around ggplot and the grammar of graphics paradigm. The software extends the popular ggplot2 framework, already familiar to many data scientists, enabling it to recog-nize the core Bioconductor flow cytometry data structures for gated and annotated cytometry data. It simplifies visualization and plotting of flow data for publication quality graphics. There are three ways to construct the ggcyto plots. Each represents a different level of complexity and flexibility. They meet the needs of various plot applications and thus are suitable for users at different levels of coding skills.

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Quality

Security

License

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Support

ggcyto has a low active ecosystem.

It has 36 star(s) with 8 fork(s). There are 14 watchers for this library.

It had no major release in the last 12 months.

There are 12 open issues and 63 have been closed. On average issues are closed in 82 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ggcyto is bioc_3.12

Quality

ggcyto has 531 bugs (0 blocker, 0 critical, 287 major, 244 minor) and 1 code smells.

Security

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

ggcyto code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ggcyto is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

ggcyto releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

It has 13560 lines of code, 0 functions and 88 files.

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

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ggcyto Key Features

No Key Features are available at this moment for ggcyto.

ggcyto Examples and Code Snippets

quick demos of some most used features

Lines of Code : 51

License : Permissive (MIT)

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library(ggcyto)
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs_orig <- load_gs(list.files(dataDir, pattern = "gs_bcell_auto",full = TRUE))
gs <- gs_clone(gs_orig)

#plot a gate by specifying the population node name (here i

Community Discussions

Trending Discussions on ggcyto

how to mimic histogram plot from flowjo in R using flowCore?

setting x-limits on ggcyto plot doesn't seem to do the trick

QUESTION

how to mimic histogram plot from flowjo in R using flowCore?

Asked 2021-May-18 at 09:27

I'm new to flowCore + R. I would like to mimic a histogram plot after gating that can be manually done in FlowJo software. I got something similar but it doesn't look quite right because it is a "density" plot and is shifted. How can I get the x axis to shift over and look similar to how FlowJo outputs the plot? I tried reading this document but couldn't find a plot similar to the one in FlowJo: howtoflowcore Appreciate any guidance. Thanks.

code snippet: ...

ANSWER

Answered 2021-May-18 at 09:27

The reason that for the "shift" is that the x axis is logarithmic (base 10) in the flowJo graph. To achieve the same result in R, add

Source https://stackoverflow.com/questions/67429156

QUESTION

setting x-limits on ggcyto plot doesn't seem to do the trick

Asked 2021-Mar-24 at 15:45

I am trying to set the x limits on a ggcyto(ggplot2) plot, but it doesn't seem to work. The x-limit that I set is squished all the way to the right and there is a lot of empty space. Not sure what else to try. I tried setting biexp scale but it looked the same.

...

ANSWER

Answered 2021-Mar-24 at 15:45

Don't have your data so can't reproduce the weird axis. I would check your data for negative values. Also the ggcyto wrapper has some restrictions on your limits.

Using an example data below, I set 2 values on the first column "FSC" to be -999, and I get a similar error:

Source https://stackoverflow.com/questions/66775113

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

Vulnerabilities

No vulnerabilities reported

Install ggcyto

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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