Unlocking the Power of R for Data Analysis and Visualization
Discover the versatility of the R programming language for statistical computing, data cleanup, visualization, and bioinformatics applications. Learn why choosing R over Excel can enhance efficiency and accuracy in data processing. Get insights into using R for replicable analysis, working with different datasets, and accessing various resources and tools. Dive into R plotting capabilities and the advantages it offers compared to traditional spreadsheet programs like Excel.
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Presentation Transcript
GETTING TO KNOW R GETTING TO KNOW R Joe Wu Bioinformatics Training and Education Program (BTEP) Bioinformatics Trainer NIH/NCI ncibtep@nih.gov 11/18/2021
Class goals Overview of R what it does, why use it instead of Excel How do we start using R Live demo oR Studio why use it and overview of interface oTutorials and learning resources oSwitching R version oSetting working directory oImporting data into R workspace and exporting data oWorking with data frames oPlotting
What is R R is an open source computer language Statistical computing Data cleanup and formatting (Tidyverse; Reshape) Graphics (base plots, ggplot2) Replicate analysis in multiple datasets Facilitates reproducible data analysis (R Markdown, Jupyter Notebook)
R biology apps Bioconductor oedgeR (RNA seq) oDESeq2 (RNA seq) obiomaRt (connecting with Ensembl resources) Seurat (single cell RNA seq analysis)
R plotting and data visualization capabilities Base plot ggplot2 https://towardsdatascience.com/top-5-r-resources-on- covid-19-coronavirus-1d4c8df6d85f
Why Choose R over Excel R is free Excel autocorrect messes up gene names https://www.nature.com/articles/d41586-021-02211-4 (ie SEPT4 becomes 4-sep if you do not tell Excel explicitly to import gene names as text) R can work with larger datasets Scripting can help avoid error due to manual copying and pasting Work faster in R
Working faster in R Excel: To create a new column with weight in grams Type in the column name Enter the calculation to convert pounds to grams Click to fill the column R: mouse_weight$WEIGHT_GRAMS <- mouse_weight$WEIGHT_POUNDS*454
To get started using R Obtain the latest R release (https://www.r-project.org) Get R Studio IDE (https://www.rstudio.com) Rswitch (https://rud.is/rswitch/) for Mac users to switch between R versions For Windows, get Rtools (https://cran.r- project.org/bin/windows/Rtools/) If using a NIH furnished Windows machine, NCI people submit a ticket to service.cancer.gov to get things installed
Note that font size set by cex is relative to a default of 1, where 1.5 indicates 50% larger 0.5 indicate 50% smaller las sets orientation for x and y axes tick labels main sets plot title cex.axis sets axis tick label font size col sets column color ylab sets y label title cex.lab sets font size for both the x and y axes names assigns bar plot column names axis.lty sets x axis line type xlab sets y label title cex.name sets font size of column names
QUESTIONS AND SUGGESTIONS ncibtep@nih.gov
