From 81f4886f911380fd4fb5613c4f7c1c712eb3d330 Mon Sep 17 00:00:00 2001
From: hpolvech <helene.polveche@ens-lyon.fr>
Date: Thu, 14 Oct 2021 09:32:32 +0200
Subject: [PATCH] exo2 Viridis
---
session_4/session_4.Rmd | 17 +++++++++++++++--
1 file changed, 15 insertions(+), 2 deletions(-)
diff --git a/session_4/session_4.Rmd b/session_4/session_4.Rmd
index 456e4ff..722c1fc 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>
--
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