iheatmapr

iheatmapr: Interactive complex heatmaps in R - Published in JOSS (2017)

https://github.com/ropensci/iheatmapr

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org
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Committers with academic emails
3 of 12 committers (25.0%) from academic institutions
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

data-visualization heatmap interactive-visualizations peer-reviewed plotly r r-package rstats

Keywords from Contributors

weather-data defra air-quality air-pollution-levels air-pollution sepa precipitation mopex kgclimateclass grdc

Last synced: 4 months ago · JSON representation

Repository

Complex, interactive heatmaps in R

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: main
Homepage: https://docs.ropensci.org/iheatmapr
Size: 21.1 MB

Statistics

Stars: 269
Watchers: 23
Forks: 36
Open Issues: 51
Releases: 5

Topics

data-visualization heatmap interactive-visualizations peer-reviewed plotly r r-package rstats

Created almost 9 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog Contributing License Codemeta

iheatmapr

iheatmapr is an R package for building complex, interactive heatmaps using modular building blocks. "Complex" heatmaps are heatmaps in which subplots along the rows or columns of the main heatmap add more information about each row or column. For example, a one column additional heatmap may indicate what group a particular row or column belongs to. Complex heatmaps may also include multiple side by side heatmaps which show different types of data for the same conditions. Interactivity can improve complex heatmaps by providing tooltips with information about each cell and enabling zooming into interesting features. iheatmapr uses the plotly library for interactivity.

While there are already plenty of awesome R packages for making heatmaps, including several great packages for making relatively simple interactive heatmaps (heatmaply and d3heatmap) or complex static heatmaps (ComplexHeatmap), iheatmapr seeks to make it easy to make complex interactive heatmaps.

Installation

To install the CRAN version of iheatmapr:

r install.packages("iheatmapr")

To install the github version of iheatmapr:

r devtools::install_github("ropensci/iheatmapr")

Example Complex Heatmap

As an example of a complex heatmap, we can make a version of the famous vaccines plot from the Wall Street Journal that has been recreated in several other heatmap frameworks in R.

A graphical demo of an iheatmap in the RStudio plot viewer

The code to create this heatmap is:

```R library(iheatmapr) data(measles, package = "iheatmapr")

mainheatmap(measles, name = "Measles
Cases", xcategorical = FALSE, layout = list(font = list(size = 8))) %>% addcolgroups(ifelse(1930:2001 < 1961,"No","Yes"), side = "bottom", name = "Vaccine
Introduced?", title = "Vaccine?", colors = c("lightgray","blue")) %>% addcollabels(ticktext = seq(1930,2000,10),font = list(size = 8)) %>% addrowlabels(size = 0.3,font = list(size = 6)) %>% addcolsummary(layout = list(title = "Average
across
states"), yname = "summary") %>%
addcoltitle("Measles Cases from 1930 to 2001", side= "top") %>% addrowsummary(groups = TRUE, type = "bar", layout = list(title = "Average
per
year", font = list(size = 8)))

```

Modular components of the plot are added in an iterative fashion to the top, right, left, or bottom of the heatmap. iheatmapr also contains a function (iheatmap) to make a fairly standard heatmap with optional dendrograms and row or column annotation heatmaps (See vignette).

All the plots aligned with the main heatmap horizontally share the same y axis and thus zooming in the y direction within the heatmap will also zoom in to those subplots. The plots aligned vertically share an x axis with that heatmap and zooming horizontally within those plots will be linked.

Hovering over the heatmaps yields a tooltip with the name of the row and column as well as the value represented.

Documentation

See the vignette for a more thorough introduction to the package.

Acknowledgements

This package includes the open source Plotly.js library, which does much of the work of making these interactive plots possible! In creating this package, I also drew inspiration & some code from the great plotly R package; in particular, the code for the iheatmapr htmlwidget is adapted from an earlier version of the plotly R package. Additionally, numerous people at Genentech helped provide feedback and guidance for this project, including but not limited to Justin Finkle, August Guang, Michael Lawrence, Gabe Becker, Steve Lianoglou, Pete Haverty... thanks to all who helped review code and/or provide feedback! This package also went through the on-boarding process for rOpensci -- thanks to the reviewers Carl Ganz and Andee Kaplan and editor Maëlle Salmon for all their helpful feedback!

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

JOSS Publication

iheatmapr: Interactive complex heatmaps in R

Published

August 14, 2017

DOI

10.21105/joss.00359

Volume 2, Issue 16, Page 359

Authors

Alicia N. Schep

Stanford University, Genentech

Sarah K. Kummerfeld

Genentech

Editor

Arfon Smith

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GitHub Events

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Watch event: 1

Last Year

Watch event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 152
Total Committers: 12
Avg Commits per committer: 12.667
Development Distribution Score (DDS): 0.217

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
AliciaSchep	a**p@g**m	119
Alicia	a**p@s**u	16
Frederick Boehm	f**m@g**m	6
Alan O'Callaghan	a**n@o**m	3
oristaszewski	1****i	1
Maëlle Salmon	m**n@y**e	1
Marcel Schilling	m**g@m**e	1
Karthik Ram	k**m@g**m	1
Jeroen Ooms	j**s@g**m	1
Jean V. Adams	J****s	1
Grace Li	g**8@b**u	1
Ahmed Mohamed	m**d@k**p	1

Committer Domains (Top 20 + Academic)

kuicr.kyoto-u.ac.jp: 1 berkeley.edu: 1 mdc-berlin.de: 1 stanford.edu: 1

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Last synced: 4 months ago

All Time

Total issues: 82
Total pull requests: 28
Average time to close issues: 3 months
Average time to close pull requests: 17 days
Total issue authors: 47
Total pull request authors: 11
Average comments per issue: 2.39
Average comments per pull request: 1.29
Merged pull requests: 22
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 3
Average time to close issues: 7 days
Average time to close pull requests: 9 days
Issue authors: 2
Pull request authors: 2
Average comments per issue: 4.33
Average comments per pull request: 1.33
Merged pull requests: 2
Bot issues: 0
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AliciaSchep (8)
dasiav7 (7)
mschilli87 (5)
halhen (3)
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lucaz88 (2)
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josruirod (2)
srsankhe (2)
romert01 (2)
ahmohamed (2)
shreyagupta0909 (2)
alanocallaghan (2)

Pull Request Authors

AliciaSchep (9)
alanocallaghan (5)
maelle (4)
fboehm (3)
ahmohamed (2)
JVAdams (1)
oristaszewski (1)
jeroen (1)
karthik (1)
mschilli87 (1)
graceli8 (1)

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question (22) enhancement (15) bug (10) maybe-fixed (2)

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Packages

Total packages: 1
Total downloads: unknown

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 5

proxy.golang.org: github.com/ropensci/iheatmapr

Documentation: https://pkg.go.dev/github.com/ropensci/iheatmapr#section-documentation
License: other
Latest release: v0.5.0
published over 5 years ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 3.2.0 depends
RColorBrewer * imports
fastcluster * imports
ggdendro * imports
htmlwidgets * imports
jsonlite * imports
knitr * imports
magrittr * imports
methods * imports
scales * imports
stats * imports
tools * imports
utils * imports
covr * suggests
datasets * suggests
htmltools * suggests
reshape2 * suggests
rmarkdown * suggests
roxygen2 * suggests
shiny * suggests
testthat * suggests
webshot * suggests

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r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

iheatmapr

Science Score: 95.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

iheatmapr

Installation

Example Complex Heatmap

Documentation

Acknowledgements

Owner

JOSS Publication

iheatmapr: Interactive complex heatmaps in R

Authors

Editor

Tags

CodeMeta (codemeta.json)

GitHub Events

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Past Year

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proxy.golang.org: github.com/ropensci/iheatmapr

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