From a1b7932d18629f057b453674838852eb0fba57de Mon Sep 17 00:00:00 2001
From: Emma Rand <emma.rand@york.ac.uk>
Date: Mon, 23 Oct 2023 17:29:00 +0100
Subject: [PATCH] a few fixes to prior study omics 3

---
 omics/week-5/Rplot001.jpg              | Bin 4227 -> 0 bytes
 omics/week-5/overview.qmd              |   2 +-
 omics/week-5/study_before_workshop.qmd |   4 ++--
 references.bib                         |   9 +++++++++
 4 files changed, 12 insertions(+), 3 deletions(-)
 delete mode 100644 omics/week-5/Rplot001.jpg

diff --git a/omics/week-5/Rplot001.jpg b/omics/week-5/Rplot001.jpg
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diff --git a/omics/week-5/overview.qmd b/omics/week-5/overview.qmd
index 80982a4..c06b941 100644
--- a/omics/week-5/overview.qmd
+++ b/omics/week-5/overview.qmd
@@ -5,7 +5,7 @@ toc: true
 toc-location: right
 ---
 
-This week we cover how to visualise and interpret the results of your differential expression analysis. The independent study will allow you to check you have what you should have following the [Omics 2: Statistical Analysis workshop](../week-4/workshop.html) and [Consolidation study](../week-4/study_after_workshop.html). It will also summarise the the methods and plots we will go through in the workshop. In the workshop, we will learn how to conduct a Principle Component Analysis (PCA) and plot the results as well as how to create a nicely formatted Volcano plot and heatmap.  
+This week we cover how to visualise and interpret the results of your differential expression analysis. The independent study will allow you to check you have what you should have following the [Omics 2: Statistical Analysis workshop](../week-4/workshop.html) and [Consolidation study](../week-4/study_after_workshop.html). It will also summarise the the methods and plots we will go through in the workshop. In the workshop, we will learn how to merge gene information into out results,  conduct a Principle Component Analysis (PCA) and plot the results as well as how to create a nicely formatted Volcano plot and heatmap.  
 
 We suggest you sit together with your group in the workshop.
 
diff --git a/omics/week-5/study_before_workshop.qmd b/omics/week-5/study_before_workshop.qmd
index 68198fd..610ad5b 100644
--- a/omics/week-5/study_before_workshop.qmd
+++ b/omics/week-5/study_before_workshop.qmd
@@ -126,7 +126,7 @@ Remind yourself of the key columns you have in the results files:
 
 ```{r}
 #| echo: false
-read_csv("results/s30_results.csv") |> glimpse()
+read_csv("results/S30_results.csv") |> glimpse()
 
 ```
 
@@ -401,7 +401,7 @@ change](figures/prog-hspc-volcano.png)
 
 ## Packages to install before the workshop
 
-**`heatmaply`** [@heatmapply] and **`ggrepel`** [@ggrepel] from CRAN in
+**`heatmaply`** [@heatmaply] and **`ggrepel`** [@ggrepel] from CRAN in
 the the normal way:
 
 ```{r}
diff --git a/references.bib b/references.bib
index fa3ab82..8580e65 100644
--- a/references.bib
+++ b/references.bib
@@ -539,4 +539,13 @@ @Manual{ggrepel
     year = {2023},
     note = {R package version 0.9.4},
     url = {https://github.com/slowkow/ggrepel},
+  }
+
+  @Article{heatmaply,
+    author = {{Galili} and {Tal} and {O'Callaghan} and {Alan} and {Sidi} and {Jonathan} and {Sievert} and {Carson}},
+    title = {heatmaply: an R package for creating interactive cluster heatmaps for online publishing},
+    journal = {Bioinformatics},
+    year = {2017},
+    doi = {10.1093/bioinformatics/btx657},
+    url = {https://academic.oup.com/bioinformatics/article-pdf/doi/10.1093/bioinformatics/btx657/21358327/btx657.pdf},
   }
\ No newline at end of file