diff --git a/session_4/session_4.Rmd b/session_4/session_4.Rmd index 456e4ff91aabd2e3d7d0fa6d72119cc8b6c802e5..722c1fc539e65aa2a6b00d858f0d24e59891f76e 100644 --- a/session_4/session_4.Rmd +++ b/session_4/session_4.Rmd @@ -431,6 +431,9 @@ library(RColorBrewer) library(ghibli) library(viridis) ``` + +## RColorBrewer & Ghibli + Using `mpg` and the 'ggplot2' package, reproduce the graph studied in session 2, 3.1: color mapping. Modify the colors representing the class of cars with the palettes `Dark2` of [RColorBrewer](https://www.datanovia.com/en/fr/blog/palette-de-couleurs-rcolorbrewer-de-a-a-z/), then `MononokeMedium` from [Ghibli](https://github.com/ewenme/ghibli). @@ -463,14 +466,24 @@ To display only Brewer palettes that are colorblind friendly, specify the option ```{r colorblindBrewer} display.brewer.all(colorblindFriendly = TRUE) ``` +## Viridis +`viridis` package provide a series of color maps that are designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. +For the next part, we will use a real data set. Anterior tibial muscle tissue was collected from 20 patients, with or without confirmed myotonic dystrophy type 1 (DM1). Illumina RNAseq was performed on these samples and the sequencing data are available on GEO with the identifier GSE86356. +First, we will use the gene count table of these samples, formatted for use in ggplot2 ( `pivot_longer()` [function](https://tidyr.tidyverse.org/reference/pivot_longer.html) ). +Open the csv file using the `read_csv2()` function. The file is located at "XXX". - - +<details><summary>Solution</summary> + <p> +```{r read_csv1} +expr_DM1 <- read_csv2("XXX/Expression_matrice_pivot_longer_DEGs_GSE86356.csv") +``` + </p> +</details>