https://github.com/pwwang/scplotter

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.
https://github.com/pwwang/scplotter

single-cell-analysis single-cell-rna-seq single-cell-sequencing visualization

Last synced: 4 days ago
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scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

• Host: GitHub
• URL: https://github.com/pwwang/scplotter
• Owner: pwwang
• License: gpl-3.0
• Created: 2024-09-03T23:03:11.000Z (4 months ago)
• Default Branch: master
• Last Pushed: 2024-12-11T04:29:59.000Z (23 days ago)
• Last Synced: 2024-12-20T03:42:36.478Z (14 days ago)
• Topics: single-cell-analysis, single-cell-rna-seq, single-cell-sequencing, visualization
• Language: R
• Homepage: https://pwwang.github.io/scplotter/
• Size: 75 MB
• Stars: 133
• Watchers: 1
• Forks: 16
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# scplotter 

`scplotter` is an R package that is built upon [`plotthis`][1]. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

## Installation

```r

remotes::install_github("pwwang/scplotter")

# or

devtools::install_github("pwwang/scplotter")

# or using conda

$ conda install pwwang::r-scplotter

```

## Credits

`scplotter` draws significant inspiration from the [`SCP`][2] package, which separates visualization from analysis and implements it in the [`plotthis`][1] package. Building on `plotthis`, `scplotter` offers advanced functions for visualizing single-cell sequencing data. Special thanks to the [`scRepertoire`][21] package for its APIs that facilitate the analysis of single-cell TCR/BCR sequencing data.

## Gallery

### scRNA-seq

[`CellDimPlot`][3]

![CellDimPlot](./man/figures/celldimplot.png)

[`CellStatPlot`][4]

![CellStatPlot](./man/figures/cellstatplot.png)

[`ClustreePlot`][5]

![ClustreePlot](./man/figures/clustreeplot.png)

[`FeatureStatPlot`][6]

![FeatureStatPlot](./man/figures/featurestatplot.png)

[`EnrichmentPlot`][7]

![EnrichmentPlot](./man/figures/enrichmentplot.png)

[`GSEASummaryPlot`][8] | [`GSEAPlot`][8]

![GSEAPlot](./man/figures/gseaplot.png)

[`VolcanoPlot`][9]

![VolcanoPlot](./man/figures/volcanoplot.png)

[`CCCPlot`][10] (Cell-Cell Communication Plot)

![CCCPlot](./man/figures/cccplot.png)

### scTCR-seq/scBCR-seq

[`ClonalVolumePlot`][11] | [`ClonalAbundancePlot`][12] | [`ClonalResidencyPlot`][13] | [`ClonalCompositionPlot`][14] | [`ClonalOverlapPlot`][15] | [`ClonalGeneUsagePlot`][16]

![clonalstat](./man/figures/clonalstat.png)

[`ClonalRarefactionPlot`][17] | [`ClonalGeneUsagePlot`][18] | [`ClonalDiversityPlot`][19] | [`ClonalPositionalPlot`][20]

![clonaldiv](./man/figures/clonaldiv.png)

[1]: https://github.com/pwwang/plotthis

[2]: https://zhanghao-njmu.github.io/SCP/index.html

[3]: https://pwwang.github.io/scplotter/reference/CellDimPlot.html

[4]: https://pwwang.github.io/scplotter/reference/CellStatPlot.html

[5]: https://pwwang.github.io/scplotter/reference/ClustreePlot.html

[6]: https://pwwang.github.io/scplotter/reference/FeatureStatPlot.html

[7]: https://pwwang.github.io/scplotter/reference/EnrichmentPlot.html

[8]: https://pwwang.github.io/plotthis/reference/gsea.html

[9]: https://pwwang.github.io/plotthis/reference/VolcanoPlot.html

[10]: https://pwwang.github.io/scplotter/reference/CCCPlot.html

[11]: https://pwwang.github.io/scplotter/reference/ClonalVolumePlot.html

[12]: https://pwwang.github.io/scplotter/reference/ClonalAbundancePlot.html

[13]: https://pwwang.github.io/scplotter/reference/ClonalResidencyPlot.html

[14]: https://pwwang.github.io/scplotter/reference/ClonalCompositionPlot.html

[15]: https://pwwang.github.io/scplotter/reference/ClonalOverlapPlot.html

[16]: https://pwwang.github.io/scplotter/reference/ClonalGeneUsagePlot.html

[17]: https://pwwang.github.io/scplotter/reference/ClonalRarefactionPlot.html

[18]: https://pwwang.github.io/scplotter/reference/ClonalGeneUsagePlot.html

[19]: https://pwwang.github.io/scplotter/reference/ClonalDiversityPlot.html

[20]: https://pwwang.github.io/scplotter/reference/ClonalPositionalPlot.html

[21]: https://github.com/ncborcherding/scRepertoire