<commit_before># Introduction

This repository maintains a list of different heatmap options in R, including fully vetted packages in CRAN / Bioconductor as well as emerging packages with devtools.

# Info
The main information is stored in the [r_heatmap_packages.tsv](https://github.com/RobersonLab/drop_it_like_its_hot_r/blob/master/r_heatmap_packages.tsv) file.

* Package - name of the package.
* Function - name of the function to plot a heatmap
* Distribution - where you can get it (base, CRAN, BioC, or devtools)
* Input - list of acceptable input
* MatrixMinInput - will it accept a matrix only as input
* SimpleFigureOut - is output a figure or interactive?
* Repository - link to development repository for the package
* Maintainer_Name - name from the package information
* Maintainer_Email - email from package information
* Twitter - handle if account known
* Status - special notes, such as in development or deprecated

Included here is a **basic** list of packages. If the input takes a single matrix and makes simple output, the package should have a demonstration output. *All of them are created from the same input!*

# Simple package table
| Type | Package | Function | Test Image |
| ---- | ------- | -------- | ---------- |
| Single matrix, simple image out | [ComplexHeatmap](https://github.com/jokergoo/ComplexHeatmap) | Heatmap | ![Heatmap](figures/ComplexHeatmap_Heatmap_base.jpeg) |
|  | [gplots](https://github.com/cran/gplots) | heatmap.2 | ![heatmap.2](figures/gplots_heatmap.2_base.jpeg) |
|  | heatmap.plus | heatmap.plus | ![heatmap.plus](figures/heatmap.plus_heatmap.plus_base.jpeg) |
|  | heatmap3 | heatmap3 | ![heatmap3](figures/heatmap3_heatmap3_base.jpeg) |
|  | NeatMap | heatmap1 | ![heatmap1](figures/NeatMap_heatmap1_base.jpeg) |
|  | [NMF](http://github.com/renozao/NMF) | aheatmap | ![aheatmap](figures/NMF_aheatmap_base.jpeg) |
|  | [pheatmap](https://github.com/cran/pheatmap) | pheatmap | ![pheatmap](figures/pheatmap_pheatmap_base.jpeg) |
|  | [stats](https://svn.r-project.org/R) | heatmap | ![heatmap](figures/stats_heatmap_base.jpeg) |
|  | [superheat](https://github.com/rlbarter/superheat) | superheat | ![superheat](figures/superheat_superheat_base.jpeg) |
|  | [vcfR](https://github.com/knausb/vcfR) | heatmap.bp | ![heatmap.bp](figures/vcfR_heatmap.bp_base.jpeg) |
| Single matrix, interactive output | [d3heatmap](https://github.com/rstudio/d3heatmap) | d3heatmap |  |
|  | [heatmaply](https://github.com/talgalili/heatmaply) | heatmaply |  |
|  | [Heatplus](https://github.com/alexploner/Heatplus) | annHeatmap2 |  |
|  | [iheatmapr](https://github.com/AliciaSchep/iheatmapr) | main_heatmap |  |
|  | [qtlcharts](https://github.com/kbroman/qtlcharts) | iheatmap |  |
| Deprecated | fheatmap | fheatmap |  |
| Multi-matrix / other | [catmaply](https://github.com/VerkehrsbetriebeZuerich/catmaply) | catmaply |  |
|  | [EnrichedHeatmap](https://github.com/jokergoo/EnrichedHeatmap) | EnrichedHeatmap |  |
|  | gapmap | gapmap |  |
|  | [ggplot2](https://github.com/tidyverse/ggplot2) | geom_tile |  |
|  | mcheatmaps | mcheatmaps |  |
|  | pairheatmap | pairheatmap |  |<commit_msg>Updated the README to see heatmapFlex<commit_after># Introduction

This repository maintains a list of different heatmap options in R, including fully vetted packages in CRAN / Bioconductor as well as emerging packages with devtools.

# Info
The main information is stored in the [r_heatmap_packages.tsv](https://github.com/RobersonLab/drop_it_like_its_hot_r/blob/master/r_heatmap_packages.tsv) file.

* Package - name of the package.
* Function - name of the function to plot a heatmap
* Distribution - where you can get it (base, CRAN, BioC, or devtools)
* Input - list of acceptable input
* MatrixMinInput - will it accept a matrix only as input
* SimpleFigureOut - is output a figure or interactive?
* Repository - link to development repository for the package
* Maintainer_Name - name from the package information
* Maintainer_Email - email from package information
* Twitter - handle if account known
* Status - special notes, such as in development or deprecated

Included here is a **basic** list of packages. If the input takes a single matrix and makes simple output, the package should have a demonstration output. *All of them are created from the same input!*

# Simple package table
| Type | Package | Function | Test Image |
| ---- | ------- | -------- | ---------- |
| Single matrix, simple image out | [ComplexHeatmap](https://github.com/jokergoo/ComplexHeatmap) | Heatmap | ![Heatmap](figures/ComplexHeatmap_Heatmap_base.jpeg) |
|  | [gplots](https://github.com/cran/gplots) | heatmap.2 | ![heatmap.2](figures/gplots_heatmap.2_base.jpeg) |
|  | heatmap.plus | heatmap.plus | ![heatmap.plus](figures/heatmap.plus_heatmap.plus_base.jpeg) |
|  | heatmapFlex | heatmap.n2 | ![heatmapFlex](figures/heatmapFlex_heatmap.n2_base.jpeg) |
|  | heatmap3 | heatmap3 | ![heatmap3](figures/heatmap3_heatmap3_base.jpeg) |
|  | NeatMap | heatmap1 | ![heatmap1](figures/NeatMap_heatmap1_base.jpeg) |
|  | [NMF](http://github.com/renozao/NMF) | aheatmap | ![aheatmap](figures/NMF_aheatmap_base.jpeg) |
|  | [pheatmap](https://github.com/cran/pheatmap) | pheatmap | ![pheatmap](figures/pheatmap_pheatmap_base.jpeg) |
|  | [stats](https://svn.r-project.org/R) | heatmap | ![heatmap](figures/stats_heatmap_base.jpeg) |
|  | [superheat](https://github.com/rlbarter/superheat) | superheat | ![superheat](figures/superheat_superheat_base.jpeg) |
|  | [vcfR](https://github.com/knausb/vcfR) | heatmap.bp | ![heatmap.bp](figures/vcfR_heatmap.bp_base.jpeg) |
| Single matrix, interactive output | [d3heatmap](https://github.com/rstudio/d3heatmap) | d3heatmap |  |
|  | [heatmaply](https://github.com/talgalili/heatmaply) | heatmaply |  |
|  | [Heatplus](https://github.com/alexploner/Heatplus) | annHeatmap2 |  |
|  | [iheatmapr](https://github.com/AliciaSchep/iheatmapr) | main_heatmap |  |
|  | [qtlcharts](https://github.com/kbroman/qtlcharts) | iheatmap |  |
| Deprecated | fheatmap | fheatmap |  |
| Multi-matrix / other | [catmaply](https://github.com/VerkehrsbetriebeZuerich/catmaply) | catmaply |  |
|  | [EnrichedHeatmap](https://github.com/jokergoo/EnrichedHeatmap) | EnrichedHeatmap |  |
|  | gapmap | gapmap |  |
|  | [ggplot2](https://github.com/tidyverse/ggplot2) | geom_tile |  |
|  | mcheatmaps | mcheatmaps |  |
|  | pairheatmap | pairheatmap |  |
{'fraction_non_alphanumeric': 0.14287947475379084, 'fraction_numerical': 0.0056276379552915425, 'mean_word_length': 4.482433590402742, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 30, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 1, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '583019', 'n_tokens_mistral': 2389, 'n_tokens_neox': 2171, 'n_words': 458}