class: center, middle, inverse, title-slide .title[ # Welcome to the R-verse ] .subtitle[ ## Setting up your computers for R ] .author[ ### Cassandra Buzby & Yen-Chung Chen ] .date[ ### 2022-06-14 ] --- # About Yen .pull-left[ ## Yen-Chung Chen - 5th-year PhD student in the Desplan lab - Work with 🪰, <svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:1em;width:1.13em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#57068c;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg>, and <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#57068c;overflow:visible;position:relative;"><path d="M439.8 200.5c-7.7-30.9-22.3-54.2-53.4-54.2h-40.1v47.4c0 36.8-31.2 67.8-66.8 67.8H172.7c-29.2 0-53.4 25-53.4 54.3v101.8c0 29 25.2 46 53.4 54.3 33.8 9.9 66.3 11.7 106.8 0 26.9-7.8 53.4-23.5 53.4-54.3v-40.7H226.2v-13.6h160.2c31.1 0 42.6-21.7 53.4-54.2 11.2-33.5 10.7-65.7 0-108.6zM286.2 404c11.1 0 20.1 9.1 20.1 20.3 0 11.3-9 20.4-20.1 20.4-11 0-20.1-9.2-20.1-20.4.1-11.3 9.1-20.3 20.1-20.3zM167.8 248.1h106.8c29.7 0 53.4-24.5 53.4-54.3V91.9c0-29-24.4-50.7-53.4-55.6-35.8-5.9-74.7-5.6-106.8.1-45.2 8-53.4 24.7-53.4 55.6v40.7h106.9v13.6h-147c-31.1 0-58.3 18.7-66.8 54.2-9.8 40.7-10.2 66.1 0 108.6 7.6 31.6 25.7 54.2 56.8 54.2H101v-48.8c0-35.3 30.5-66.4 66.8-66.4zm-6.7-142.6c-11.1 0-20.1-9.1-20.1-20.3.1-11.3 9-20.4 20.1-20.4 11 0 20.1 9.2 20.1 20.4s-9 20.3-20.1 20.3z"/></svg>. ] -- .pull-right[ <img src="img/Dm3_1-4.png" width="75%" /><img src="img/L3_optic_lobe.png" width="75%" /> ] --- # About Cassandra .pull-left[ ## Cassandra Buzby - 5th-year PhD student in the Siegal lab - Studies gene interactions using budding yeast and analyzes the data in R (which you'll see later!) ] .pull-right[ <img src="img/cb.jpg" width="75%" /> ] --- layout: true # Why are we here? .pull-left[ ## Because - Biology has become big - We need multiple perspectives - We need to challenge our premise ] --- .pull-right[ <img src="img/scrna.png" width="1504" /> ] .legend[ [1] [Angerer _et al._ (2017)](https://doi.org/10.1016/j.coisb.2017.07.004) ] --- .pull-right[ <img src="img/gb.png" width="1392" /> ] .legend[ [1] [GenBank and WGS Statistics](https://www.ncbi.nlm.nih.gov/genbank/statistics/) ] --- .pull-right[ ## Therefore - Data wrangling (3) - Data visualization (2) - Statistics and modeling (2) ] --- layout: true # Do (not) bother to pick a language --- - Languages are often more similar than different -- ```r # R model <- lm(x = data[["x"]], y = data[["y"]]) ``` -- ```python # Python model = LinearRegression() model.fit(x = data['x'], y = data['y']) ``` -- ```julia # julia model = lm(@formula(y~x), data) ``` -- ```octave # MATLAB model = fitlm(data, 'y', 'x'); ``` --- - Use whatever tool your peers are using -- - Use what is popular in your field -- - Use what addresses your immediate need --- layout:true # Why R? --- .pull-left[ ## Pros - R is intuitive - R has a strong community in genomics and statistics - R is very visual ] -- .pull-right[ ## Cons - R could be counterintuitive in a programming sense - R is less powerful for building computationally heavy tools ] --- layout: false # Goals of this workshop - Help you to do whatever you want to do with your data in R -- - Give you the lever to work with thousands to millions of data entries (`dplyr` and `tidyr`) -- - Visualize your data in multiple perspectives with minimal struggle (`ggplot2`) -- - Test your hypotheses with statistics --- class: inverse, middle, center, section-title # Questions?