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resources.Rmd
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resources.Rmd
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---
title: Resources
output:
html_document:
theme: cosmo
highlight: textmate
css: style.css
toc: true
toc_depth: 1
toc_float: true
---
# Books
## Data visualization using R (optional)
[<img style="height:150px; width:112px; border: 3px solid black;" src="img/wilke.jpg"/>](https://serialmentor.com/dataviz/index.html){target=_blank}
[<img src="img/healy.jpg" style="border: 3px solid black;height:150px; width:112px"/>](https://socviz.co/){target=_blank}
Clicking on the covers will send you to the free online versions of each book
## R fundamentals (optional)
[<img style="height:150px; width:112px; border: 3px solid black" src = "img/r4ds.png"/>](https://r4ds.had.co.nz/){target=_blank}
## R Markdown (optional)
[
<img src='img/rmd.png' style="width:112px; height:150px; border:3px solid black" />
](https://bookdown.org/yihui/rmarkdown/){target=_blank}
Of partcular interest to us will be chapters on [HTML
documents](https://bookdown.org/yihui/rmarkdown/html-document.html){target=_blank} and [HTML
Presentations](https://bookdown.org/yihui/rmarkdown/ioslides-presentation.html){target=_blank}
### Other books
- [The Truthful Art: Data, Charts, and Maps for Communication](http://www.thefunctionalart.com/p/the-truthful-art-book.html){target=_blank} by Albert Cairo
- [FLowing Data](https://www.amazon.com/gp/product/0470944889/){target=_blank} by Nathan Yau
- [R Graphics Cookbook](http://www.cookbook-r.com/Graphs/){target=_blank} by Winston Chang
- [Modern Statistics for Modern Biology](http://web.stanford.edu/class/bios221/book/index.html){target=_blank} by Susan Holmes and Wolfgang Huber
-----
# Web references
## Data viz
- [ggplot2 reference](https://ggplot2.tidyverse.org/){target=_blank}: The definitive guide to ggplot2. Check out the pages for the different functions for great examples
- [R graph gallery](https://www.r-graph-gallery.com/): Example-filled site for different R-based graphs, specially in ggplot. The ads can be a bit irritating, but the content is great.
- [htmlwidgets for R](https://www.htmlwidgets.org/): Reference and gallery for different Javascript interactive graphics libraries that have been ported to R
- Bioinformatics-related
- [Bioconductor packages](http://www.bioconductor.org/packages/release/BiocViews.html#___Visualization){target=_blank} for visualization
-[heatmaply](https://cran.r-project.org/web/packages/heatmaply/vignettes/heatmaply.html): R package for interactive heatmaps
- [manhattanly](https://cran.r-project.org/web/packages/manhattanly/): R package for interactive Manhattan plots
- [Graphics chapter](http://web.stanford.edu/class/bios221/book/Chap-Graphics.html) from _Modern Statistics for Modern Biology_ by Holmes and Huber
## R programming
-
- Bioinformatics-related
- [RNAseq analysis in R](http://combine-australia.github.io/RNAseq-R/)
- [GEN 242](http://girke.bioinformatics.ucr.edu/GEN242/index.html) course website from University of California Riverside
- [RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR](https://f1000research.com/articles/5-1408/v3): Open review paper on using R for RNA-seq analysis
- [Analysis of single cell RNA-seq data](https://hemberg-lab.github.io/scRNA.seq.course/index.html) from Hember lab
-----
# Web resources
- [Flowing Data](https://www.flowingdata.com): This is one of my favorite sites for learning data viz. There are several [tutorials](https://flowingdata.com/category/tutorials/) in R for different graphics, as well as other languages. Nathan Yau, who runs the website, also has 2 excellent [books](https://flowingdata.com/books/) on data viz, as well as a few self-guided [courses](https://flowingdata.com/courses/) for data viz in R.
- [JunkCharts](https://junkcharts.typepad.com): Critiques of chartjunk + junk art
- [I want hue](https://medialab.github.io/iwanthue/): Colors for data scientists
## Infographics
- [BusinessPundit’s Guide to Infographics](https://www.businesspundit.com/guide-to-infographics/)
- [A complete exploratory data analysis and visualization for text data](https://towardsdatascience.com/a-complete-exploratory-data-analysis-and-visualization-for-text-data-29fb1b96fb6a)
-
-----
# ggplot2-related resources {#ggplot}
- [ggplot2 reference](https://ggplot2.tidyverse.org/){target=_blank}: The definitive guide to ggplot2. Check out the pages for the different functions for great examples
- [ggplot2 cheatsheet](https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf){target=_blank}
- [Cheatsheets](https://www.r-graph-gallery.com/cheatsheet/){target=_blank} from the [R-Graph Gallery](https://www.r-graph-gallery.com/){target=_blank}
- [Themes to improve your ggplot figures](https://rfortherestofus.com/2019/08/themes-to-improve-your-ggplot-figures/)