Vallo Varik committed May 16, 2022 1 2 3 4 5 6 7 8 9 10 11 ``````--- title: "32 drugs" output: md_document: preserve_yaml: FALSE fig_width: 7 fig_height: 5 toc: yes toc_depth: 2 --- `````` Vallo Varik committed May 16, 2022 12 ``````# Motivation `````` Vallo Varik committed May 16, 2022 13 `````` `````` Vallo Varik committed May 16, 2022 14 ``````Getting up to speed with R using dose-response for 32 drugs against 6 `````` Vallo Varik committed May 16, 2022 15 ``````bacterial strains. `````` Vallo Varik committed May 16, 2022 16 17 18 19 `````` # Tasks `````` Vallo Varik committed May 17, 2022 20 ``````In the following, we go through the most common steps in data analysis: `````` Vallo Varik committed May 17, 2022 21 ``````exploration and transformation (i.e. deriving new variables). Integral to both `````` Vallo Varik committed May 17, 2022 22 ``````steps is visualization i.e. making graphs. `````` Vallo Varik committed May 16, 2022 23 24 25 `````` ## Explore `````` Vallo Varik committed May 17, 2022 26 27 28 29 30 ``````1. Plot growth curves following raw OD in time. Input [data](doc/tasks/01_dat.csv) and expected [output](doc/tasks/01_out.pdf) plot are provided. The data is for azithromycin against _S. flexneri_ M90T from day 2022-05-04 (first replicate). _A tip: Use `facet_wrap` with `ncol = 1` argument to have different concentrations on separate plots._ `````` Vallo Varik committed May 16, 2022 31 `````` `````` Vallo Varik committed May 17, 2022 32 33 ``````2. Try again, now with [data](doc/tasks/02_dat.csv) from two days (let us plot days in different color). In addition, transform the y-axis to logarithmic `````` Vallo Varik committed May 17, 2022 34 35 36 `````` scale. Expected [output](doc/tasks/02_out.pdf). _A tip: you need to turn the `Date` variable into a factor._ `````` Vallo Varik committed May 17, 2022 37 38 39 40 41 ``````3. Once more, now with [data](doc/tasks/03_dat.csv) from three days. Expected [output](doc/tasks/03_out.pdf). You will encounter an issue because there were two biological replicates on that day. There are multiple ways to overcome this, but for now, I recommend to solve by using `group` parameter of `aes` e.g. `ggplot(aes(..., group = Plt))`.``````