diff --git a/omics/week-5/Rplot001.jpg b/omics/week-5/Rplot001.jpg deleted file mode 100644 index fd0b397..0000000 Binary files a/omics/week-5/Rplot001.jpg and /dev/null differ 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