Merge pull request #107 from ARTbio/volcano_plots

Finish with Volcano and recap potential issues of week 04

docs/bulk_RNAseq-IOC/29_volcano.md

@@ -1,24 +1,97 @@
-![](images/galaxylogo.png)
-
-# `Volcano Plot create a volcano plot`
-
-----
-![](images/tool_small.png)
-
-  1. Select the `Volcano Plot create a volcano plot` tool with the following parameters:
-      - `Specify an input file`: the DESeq2 result file
-      - `FDR (adjusted P value)`: Column: 7
-      - `P value (raw)`: Column: 6
-      - `Log Fold Change`: Column: 3
-      - `Labels`: Column: 1
-      - `Points to label`: Significant
-          - `Only label top most significant`: 15
-      - `Plot Options`:
-          - `Label Boxes`: No
-          - `Labels for Legend`: Down,NotSig,Up
-  2. `Execute`
-
-  You should obtain something like :
-
+# Volcano Plots
+
+## Introduction
+Volcano plots are used to quickly identify changes in large data sets composed of
+replicate data. They are therefore perfectly suited to summarizing graphically the results
+returned by DE analysis packages.
+
+Volcano plots plot significance versus fold-change on the y and x axes, respectively. Thus,
+they combine a measure of statistical significance from a statistical test (e.g., a p or 
+p-adj value from a DE model) with the magnitude of the change, enabling quick visual
+identification of those data-points (e.g. genes) that display large magnitude changes
+that are also statistically significant.
+
+The statistical significance metrics used in volcano plots of gene DE is most often the
+p-value adjusted for multi-testing (p-adj).
+
+Last but not least, the volcano plots provide a convenient way to show the dynamics of DE
+in the experiment. In other words, they show the overall magnitude of the changes in gene
+expression, ==as seen through the analysis of read count changes==.
+
+## Application to the use-case PRJNA630433
+
+We are going to make volcano plots from the results by DESeq2, edgeR and limma-voom,
+respectively.
+
+You should do it for your own analysis too !
+
+- [x] Thus, here, we are going to create a new `PRJNA630433 volcano plots` history.
+- [x] and copy the DE reports from the 3 histories `PRJNA630433 DESeq2 analysis`,
+  `PRJNA630433 edgeR analysis` and `PRJNA630433 limma analysis`, respectively.
+- [x] Remember that for this operation, the most convenient way is to work from the
+  "Destination" history (`PRJNA630433 volcano plots`), and to use the `copy dataset` menu,
+  while navigating sequentially through the various "source histories" mentioned above.
+- [x] Following this way, copy `DESeq2 Results Tables` from `PRJNA630433 DESeq2 analysis`
+  (it is a collection of three datasets), `edgeR DE tables` from `PRJNA630433 edgeR analysis`
+  and `limma on data 4, data 3, and others: DE tables` from `PRJNA630433 limma analysis`.
+
+## Use of the Volcano Plot Galaxy tool for DESeq2 results
+
+!!! info "![](images/tool_small.png){width="25" align="absbottom"} `DESeq2` settings"
+    - Specify an input file
+
+        --> Click the collection icon and select `DESeq2 Results Tables`
+    - File has header?
+
+        --> `Yes`
+    - FDR (adjusted P value)
+
+        If you deploy the datasets in the collection, you'll see that the P-adj is in
+        column 7
+
+        --> `Column: 7`
+    - P value (raw)
+
+        --> `Column: 6`
+    - Log Fold Change
+
+        --> `Column: 3`
+    - Labels
+
+        --> `Column: 1` (these are the gene names)
+    - Significance threshold
+
+        --> select `0.05` this is only a display parameter.
+    - LogFC threshold to colour 
+
+        --> `2` ie gene with a fold-change higher than 4 or lower than 1/4
+    - Points to label
+
+        --> select `Significant`
+    - Only label top most significant
+
+        --> Let's take the `10` most significant genes for comparison with other callers
+    - Plot Options
+
+        --> Just check `Label Boxes` with `Yes`, leave the rest unchanged
+    - Output Options
+
+        --> Leave `Output Rscript?` to `No`
+    - `Run Tool`
+
+:warning: Rename the generated collection `Volcano Plot on collection 4: PDF` to
+`Volcano Plots on DESeq2 results`
+
+## Repeat the same operation for edgeR and limma-voom
+
+:warning: Be careful that the columns numbers for P-adj, P-val and log2FC may change from
+one caller to the other ! You may check this by deploying the datasets in the corresponding
+collections.
+
+:warning: rename the Volcano plot collections to `Volcano Plots on edgeR results` and
+`Volcano Plots on limma results`, respectively.
+
+## Comparison of DESeq2, edgeR and limma Volcano plots for the condition Mo versus Dc
+
 ![](images/volcano.png)
 

docs/bulk_RNAseq-IOC/30_exercices_week_04_review.md

@@ -1,30 +1,11 @@
-## Issues with Slack ?
+## Issues with DESeq2 ?
 
-## Issues with GitHub ?
-- [x] Does everyone have a GitHub ID ? 
-- [x] Was everyone able to create a readme file and make a pull request to the repository
-      [ARTbio_064_IOC_Bulk-RNAseq](https://github.com/ARTbio/ARTbio_064_IOC_Bulk-RNAseq) ?
-- [x] Was everyone able to retrieve the galaxy workflow file (the one that you have
-      generated during the first online meeting, with an extension .ga) and to add it in
-      the repository
-      [ARTbio_064_IOC_Bulk-RNAseq](https://github.com/ARTbio/ARTbio_064_IOC_Bulk-RNAseq) ?
+## Issues with edgeR ?
 
-## Data upload in PSILO, then in Galaxy from Psilo
-- [x] Did everyone upload the necessary data in its
-      [PSILO account](https://psilo.sorbonne-universite.fr) ?
-- [x] Did everyone succeed to create direct download links ? 
-- [x] Did everyone succeed to transfer its PSILO data into a Galaxy story `Input dataset`
-      in its Galaxy account ?
+## Issues with limma-voom ?
 
-## Issues following the Galaxy training ?
+## Issue with data manipulations ?
 
-[training to collection operations](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/collections/tutorial.html)
+## Issue with Venn diagrams
 
-- Check whether `Relabel identifiers` tool is understood
-
-- Check whether `Extract element identifiers` tool is understood. Is the output dataset
-  from this tool uploaded in the appropriate GitHub folder ?
-
-## Check input datasets histories of the participants
-
-... and their ability to create appropriate collection for the analysis
+## Issue with Volcano Plots ?