Commit 3fe83dfd authored by gohr's avatar gohr
Browse files

moves description of GSEA summary plots to top of website and corrects this description

parent babb412a
......@@ -169,7 +169,7 @@ category_exists <- function(category, species) {
#' For each pre-defined gene set GSEA then determines the positions of genes from the set in the sorted list of genes and statistically assesses if these genes are enriched in the beginning (among the up-regulated genes) or end (among the down-regulated genes) of the list or if they spread rather randomly across the list of sorted genes.
#'
#' For each pre-defined gene set GSEA outputs a p value and q value (FDR) measuring how significantly the gene set deviate from being randomly spread across the sorted gene list.
#' If several gene sets (eg. more than 30) are tested, we recommend to consider p and q values together and focus on results with p value < 0.05 (or < 0.01) and a q value < 0.25 (or <0.2 or <0.1).
#' If several gene sets (eg. more than 30) are tested, we recommend to consider p and q values together and focus on results with p value < 0.05 (or < 0.01) and a q value < 0.1 (or <0.05).
#'
#' In addition, GSEA outputs for each tested gene set an enrichment score (ES) and a normalized (to the size of each tested gene set) enrichment score (NES) that is comparable among gene sets of different size; a positive NES says that the tested gene set is enriched among the up-regulated genes at the beginning of the sorted gene list, a negative NES says that the tested gene set is enriched among the down-regulated genes at the end of the sorted gene list.
#'
......@@ -177,6 +177,11 @@ category_exists <- function(category, species) {
#'
#' <img src="https://git.mpi-cbg.de/bioinfo/ngs_tools/uploads/6cf3f282c707fcd0e00df0374b8b55d9/gsea_example.png" width="670" height="380">
#' <img src="https://git.mpi-cbg.de/bioinfo/ngs_tools/uploads/251f7dafe6249a1fa000c54ce50da58b/gsea_negES.png" width="670" height="380">
#'
#' An example plot that summarizes GSEAs for several gene sets at once is shown below. It depicts the enrichment statistic for the gene of each tested gene set along the sorted list of genes.
#' Again, a concentration of lines with positive y value at the beginning of the list indicates enrichment of the tested gene set among the up-regulated genes, while lines with negative y value at the end indicate enrichment among down-regulated genes.
#'
#' ![gsea_table_example](https://git.mpi-cbg.de/bioinfo/ngs_tools/uploads/5acc91e05974178323e9663233e6d035/gsea_table_example.png)
#'
#' More details: https://www.genepattern.org/modules/docs/GSEA/14
......@@ -331,16 +336,6 @@ fgseaRes_l <- ranks_l %>%
# ==========================================================================
# Plots
# ==========================================================================
#' For a gene set to be considered enriched we used a p-adjusted value cutoff of `r qcutoff`. The plots are for those sets that passed the cut-off.
#'
#' We can have an overview of the pathway enrichment by plotting the normalized enrichment score (NES) and p-adjusted values for each of the top enriched pathways. A positive NES indicates gene set enrichment at the top of the ranked list; a negative NES indicates gene set enrichment at the bottom of the ranked list.
#' **Note:** At the top of the list (left of x-axis) are the down-regulated genes, and at the bottom the up-regulated (right of x-axis).
#' Reference: https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html
#'
#' Regarding the plots saved as png in the `figure` folder, they show the value of the ranking metric as you move down the list of ranked genes. So the x-axis is the metric used to rank the genes (-log10(pvalue) multiplied by -1 or 1 depending on the fold-change) and the y-axis is the gene rank. Only genes part of the pathway are shown. In essence this is a visually appellative plot but not very informative. Here is an example:
#'
#'![gsea_table_example](https://git.mpi-cbg.de/bioinfo/ngs_tools/uploads/5acc91e05974178323e9663233e6d035/gsea_table_example.png)
#'
#'The information contained in this plot is also in the final results table present in the report and in the results folder (`fgseaRes.txt`).
#'
#+ results='asis'
......
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