Initial commit

DESCRIPTION

+Package: TopGOwrapper
+Version: 1.0.0
+Title: A Wrapper to perform TopGO enrichment analysis
+Licence: "aGPL3"
+Authors@R: person("Nicolas", "Fontrodona",
+                  email = "nicolas.fontrodona@ens-lyon.fr",
+                  role = c("aut", "cre"))
+Description: The package provides a way to easyly make TopGO enrichment analysis
+Depends:
+  R (>= 4.1.2),
+Imports:
+  topGO (>= 2.46.0),
+  org.Hs.eg.db (>= 3.14.0),
+  argparser (>= 0.7.1),
+  forcats (>= 0.5.1),
+  readr (>= 2.1.2),
+  dplyr (>= 1.0.7),
+  ggplot2 (>= 3.3.5)
+LazyData: true
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.0
+Suggests:
+    testthat

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(build_figure)
+export(cli_function)
+export(cli_run_topgo)
+export(get_gene_list)
+export(load_input)
+export(run_topgo)
+export(top_go_analysis)
+import(argparser)
+import(dplyr)
+import(forcats)
+import(ggplot2)
+import(org.Hs.eg.db)
+import(readr)
+import(topGO)

R/figure.R

+#' Produce figure displaying the top enriched go term
+#'
+#' @param top_go_result dataframe containing top_go results
+#' @param go_term_type The go term type of the figure
+#' @param outfile File were the figure will be created
+#' @import ggplot2
+#' @import dplyr
+#' @import forcats
+#' @export
+build_figure <- function(top_go_result, go_term_type, outfile) {
+    if (go_term_type == "BP") {
+        go_name <- "Biological Process"
+    } else if (go_term_type == "MF") {
+        go_name <- "Molecular Function"
+    } else {
+        go_name <- "Cellular Component"
+    }
+    top_go_result$fish <- as.numeric(gsub("< ", "", top_go_result$fish))
+    top_go_result <- top_go_result %>%
+        mutate(significance = -log10(fish), ft = paste(GO.ID, ":", Term)) %>%
+        filter(fish <= 0.05) %>%
+        arrange(desc(significance)) %>%
+        ggplot(top_go_result, mapping = aes(
+            x = significance, y = fct_reorder(ft, significance),
+            size = Significant,
+            color = Term
+        )) +
+        geom_point() +
+        xlab("-log10(pvalue)") +
+        ylab(go_name) +
+        theme_bw() +
+        theme(
+            legend.position = "none"
+        )
+    ggsave(outfile, width = 6, height = 5)
+}

R/load_df.R

+#' Load the file containing differentially or not expressed genes
+#'
+#' @param de_file the file containing differentially or not expressed genes
+#'
+#' @return The loaded file with a gene column
+#'
+#' @import dplyr
+#' @export
+load_input <- function(de_file) {
+    df <- read.table(de_file, sep = "\t", header = T)
+    if (!"gene" %in% colnames(df)) {
+        df$gene <- rownames(df)
+    }
+    df <- dplyr::tibble(df)
+    return(df)
+}

R/main.R

+#' Perform all go term enrchment analysis
+#'
+#' @param de_table tibble containing DESeq2 enrichment score
+#' @param output_folder Folder where the results will be created
+#' @param id_kind The kind of id to use in the topGO analysis. Must correspond
+#' to the ids defined in gene column of de_file
+#' @param top The number of most enriched GO term to return
+#' @param alpha The padj threshold of a genes to be considered a significant
+#' @param log2fc_threshold The threshold above which we want to consider
+#' de-genes. It must be positive
+#' @return The table containing the go enrichment analysis performed by topGO
+#' @import dplyr
+#' @import readr
+#' @export
+run_topgo <- function(de_table, output_folder, id_kind, top, alpha,
+                      log2fc_threshold) {
+    for (go_term_type in c("BP", "MF", "CC")) {
+        for (regulation in c("down", "up", "all")) {
+            res <- top_go_analysis(
+                de_table, id_kind, go_term_type, regulation, top,
+                alpha, log2fc_threshold
+            )
+            res <- res %>%
+                as_tibble() %>%
+                select(-Expected)
+            if (regulation == "all") {
+                tmp_name <- "all_de_genes"
+            } else {
+                tmp_name <- paste0(regulation, "_regulated_genes")
+            }
+            stem_name <- paste0(
+                tmp_name, "_", go_term_type, "_a", alpha, "_lfct",
+                log2fc_threshold, "_top", top
+            )
+            txt_file <- paste0(output_folder, "/", stem_name, ".txt")
+            write_tsv(res, txt_file)
+            figure_file <- paste0(output_folder, "/", stem_name, ".pdf")
+            build_figure(res, go_term_type, figure_file)
+        }
+    }
+}
+
+
+
+#' Cli TopGO Wrapper
+#'
+#' @details perform a TopGO analysis using fisher statistics on human go term
+#' for:
+#' 1. Each go term type: BP, MF, CC
+#' 2. Down-regulated, Up-regulated and all differentially expressed genes
+#'
+#' @export
+cli_run_topgo <- function() {
+    cli <- cli_function()
+    if (!dir.exists(cli$output)) {
+        if (dir.exists(dirname(cli$output))) {
+            dir.create(cli$output, showWarnings = F)
+        } else {
+            stop(paste0(cli$output, "or its parent must exist !"))
+        }
+    }
+    if (!file.exists(cli$de_file)) {
+        stop("The file --de_file doesn't exists !")
+    }
+    de_table <- load_input(cli$de_file)
+
+    run_topgo(
+        de_table, cli$output, cli$id, cli$top, cli$alpha,
+        cli$log2fc_threshold
+    )
+}

R/parser.R

+#' Parse  the command line arguments
+#'
+#' Parse the command line arguments and return an object through which all
+#' given arguments are stored
+#' @import argparser
+#' @export
+cli_function <- function() {
+    # Create a parser
+    p <- arg_parser(paste0(
+        "Wrapper to perform TopGO enrichment analysis ",
+        "For now, it only work on human genes, with the fisher enrichment",
+        " method. Moreover, all genes in that files are used as the gene universe"
+    ))
+
+    # Add command line arguments
+    p <- add_argument(p, "--de_file",
+        type = "character",
+        help = paste0(
+            "A file containing deseq2 enrichment analysis.",
+            "All genes must be defined in this file event",
+            "those not differentially expressed"
+        )
+    )
+    p <- add_argument(p, "--id",
+        type = "character",
+        help = paste0(
+            "The id identifying the genes in de_file. It can take",
+            " the following values: 'entrez', 'genbank', 'alias', 'ensembl',",
+            " 'symbol', 'genename', 'unigene'. Defaults to 'symbol' "
+        ),
+        default = "symbol"
+    )
+    p <- add_argument(p, "--output",
+        short = "-o", type = "character",
+        help = "folder were the results will be created",
+        default = "."
+    )
+    p <- add_argument(p, "--top",
+        short = "-t", type = "numeric",
+        help = "The number of top go term to display", default = 20
+    )
+
+
+    p <- add_argument(p, "--alpha",
+        short = "-t", type = "numeric",
+        help = paste0(
+            "The padj threshold in de_file below which",
+            " genes are considered as differentially expressed",
+            " defaults to 0.05"
+        ), default = 0.05
+    )
+
+    p <- add_argument(p, "--log2fc_threshold",
+        short = "-t", type = "numeric",
+        help = paste0(
+            "The log2fc threshold in de_file above which( in absolute value)",
+            " genes are considered as differentially expressed",
+            ", defaults to 0"
+        ), default = 0
+    )
+
+    # Parse de command line arguments
+    argv <- argparser::parse_args(p)
+    if (is.null(argv$de_file)) {
+        msg <- paste0(
+            "Argument --de_file is required !,",
+            " see --help for more information."
+        )
+        stop(msg)
+    }
+    return(argv)
+}

R/topGO_analysis.R

+#' Get the gene list vector needed for differential expression
+#'
+#' @param de_table tibble containing DESeq2 enrichment score
+#' @param regulation The regulation of the gene of interest 'down', 'up' 'all'
+#' where 'down to perform enrichment for down-regulated genes, 'up'
+#' to perform enrichement for up-regulated genes and 'all' to perform
+#' enrichment for all differentially expressed genes
+#' @param alpha The padj threshold of a genes to be considered a significant
+#' @param log2fc_threshold The threshold above which we want to consider
+#' de-genes. It must be positive
+#' @return the named vector used to build the topGO object
+#'
+#' @export
+get_gene_list <- function(de_table, regulation, alpha, log2fc_threshold) {
+    if (regulation == "down") {
+        gene_list <- as.integer(de_table$padj <= alpha &
+            de_table$log2FoldChange <= -log2fc_threshold)
+    } else if (regulation == "up") {
+        gene_list <- as.integer(de_table$padj <= alpha &
+            de_table$log2FoldChange >= log2fc_threshold)
+    } else {
+        gene_list <- as.integer(de_table$padj <= alpha & de_table$log2FoldChange > abs(log2fc_threshold))
+    }
+    names(gene_list) <- de_table$gene
+    return(gene_list)
+}
+
+
+#' Perform the TopGO analysis
+#'
+#' @param de_table tibble containing DESeq2 enrichment score
+#' @param id_kind The kind of id to use in the topGO analysis. Must correspond
+#' to the ids defined in gene column of de_file
+#' @param go_term_type The type of go term to use in the analysis
+#' @param regulation The regulation of the gene of interest 'down', 'up' 'all'
+#' where 'down to perform enrichment for down-regulated genes, 'up'
+#' to perform enrichement for up-regulated genes and 'all' to perform
+#' enrichment for all differentially expressed genes
+#' @param top The number of most enriched GO term to return
+#' @param alpha The padj threshold of a genes to be considered a significant
+#' @param log2fc_threshold The threshold above which we want to consider
+#' de-genes. It must be positive
+#' @return The table containing the go enrichment analysis performed by topGO
+#' @import topGO
+#' @import org.Hs.eg.db
+#' @export
+top_go_analysis <- function(de_table, id_kind, go_term_type, regulation, top,
+                            alpha, log2fc_threshold) {
+    gene_list <- get_gene_list(de_table, regulation, alpha, log2fc_threshold)
+    GOdata <- new("topGOdata",
+        ontology = go_term_type,
+        allGenes = gene_list,
+        nodeSize = 10,
+        annot = annFUN.org,
+        mapping = "org.Hs.eg.db",
+        ID = id_kind,
+        geneSel = function(score) {
+            return(score == 1)
+        }
+    )
+    results.f <- runTest(GOdata, algorithm = "classic", statistic = "fisher")
+    res <- GenTable(GOdata, fish = results.f, orderBy = "fish", topNodes = top)
+    return(res)
+}

README.md

+# TopGO_wrapper
+
+
+# Description
+
+This is an R package dedicated to perform GO enrichment analysis from  deseq2 differential expression file
+
+# Dependencies
+
+Depends:
+  R (>= 4.1.2),
+Imports:
+  topGO (>= 2.46.0),
+  org.Hs.eg.db (>= 3.14.0),
+  argparser (>= 0.7.1),
+  forcats (>= 0.5.1),
+  readr (>= 2.1.2),
+  dplyr (>= 1.0.7),
+  ggplot2 (>= 3.3.5)
+
+
+# Installation
+
+To install this package, the `devtools` package must be installed.
+
+Run in R the following command to install the package:
+
+```R
+> library(devtools)
+> install_gitlab("LBMC/regards/topgo-wrapper", host = "https://gitbio.ens-lyon.fr", quiet = FALSE)
+```
+
+# Limitations
+
+For not, it only works with human datasets and only performs GO enrichment using the 'classic' topGO algorithm and the 'fisher' statistic
+
+
+# Usage
+
+## With a command line interface (CLI) script
+
+First, you must create an R file containing only the following code:
+
+```R
+# my_R_file.R
+
+#!/bin/Rscript
+#!/bin/Rscript
+
+library('TopGOqwrapper')
+library('topGO')
+library('org.Hs.eg.db')
+cli_run_topgo()
+```
+
+Then you can type the following commands to see if everything works:
+
+```console
+$ Rscript my_R_file.R --help
+...
+usage: test.R [--] [--help] [--opts OPTS] [--de_file DE_FILE] [--id ID]
+       [--output OUTPUT] [--top TOP] [--alpha ALPHA]
+       [--log2fc_threshold LOG2FC_THRESHOLD]
+
+Wrapper to perform TopGO enrichment analysis For now, it only work on
+human genes, with the fisher enrichment method. Moreover, all genes in
+that files are used as the gene universe
+
+flags:
+  -h, --help          show this help message and exit
+
+optional arguments:
+  -x, --opts          RDS file containing argument values
+  -d, --de_file       A file containing deseq2 enrichment analysis.All
+                      genes must be defined in this file eventthose not
+                      differentially expressed
+  -i, --id            The id identifying the genes in de_file. It can
+                      take the following values: 'entrez', 'genbank',
+                      'alias', 'ensembl', 'symbol', 'genename',
+                      'unigene'. Defaults to 'symbol' [default: symbol]
+  -o, --output        folder were the results will be created [default:
+                      .]
+  -t, --top           The number of top go term to display [default:
+                      20]
+  --alpha             The padj threshold in de_file below which genes
+                      are considered as differentially expressed
+                      defaults to 0.05 [default: 0.05]
+  --log2fc_threshold  The log2fc threshold in de_file above which( in
+                      absolute value) genes are considered as
+                      differentially expressed, defaults to 0 [default:
+                      0]
+```
+
+The de_file parameter must correspond to a file with the following structure:
+
+| gene   | baseMean         | log2FoldChange     | lfcSE             | stat                | pvalue             | padj              |
+| ------ | ---------------- | ------------------ | ----------------- | ------------------- | ------------------ | ----------------- |
+| A1BG   | 240.956914340076 | 0.133226932617053  | 0.328043296485508 | 0                   | 1                  | 1                 |
+| A2M    | 9636.70629697928 | -0.595284877763812 | 0.502037280842549 | -0.0204862829042333 | 0.983655454438162  | 1                 |
+| A4GALT | 402.374065197262 | -1.0931216879495   | 0.347107578223515 | -1.46387379540962   | 0.143228434481562  | 0.976692858834766 |
+| AAAS   | 226.084731795302 | 2.97777448404702   | 1.26846531308784  | 1.88635389502473    | 0.0592472810840546 | 0.549734319535217 |
+
+
+
+1. The `gene` columns must contain the ID of the gene. you can specify the type of ID with the `--id` parameter
+2. The `baseMean` column  correspond the the mean gene expression across samples
+3. The `log2FoldChange` column, corresponds to the log2FoldChange of expression between conditions
+4. The `padj` column, corresponds to the pvalues adjusted
+
+Note that only `gene`, `log2FoldChange` and `padj` column are required
+
+The columns must be `tab-separated`.
+
+Note that the column gene can corresponds to rownames of the table
+
+** WARNING: This input file must contain ALL genes whether they are differentially expressed or not. Indeed, all genes defined in this file are used as the gene universe. **
+
+# output
+
+Here a description of the results file you get by running the package:
+
+```
+result_folder
+├── [REG]_genes_[GOTYPE]_a[ALPHA]_lfc[LFCT]_top[NUM].pdf
+└── [REG]_genes_[GOTYPE]_a[ALPHA]_lfc[LFCT]_top[NUM].txt
+```
+
+Where:
+- `REG`: Can be equal to down_regulated, up_regulated or all_de. When `REG` is
+   - `down_regulated`: Only consider the down-regulated (`padj` <= `ALPHA` & `log2FoldChange` <= `LFCT`) genes...
+   -  `up_regulated`: Only consider the up-regulated (`padj` <= `ALPHA` & `log2FoldChange` >= `LFCT`) genes...
+   -  `all_de`: Consider all differentially expressed (`padj` <= `ALPHA` & `log2FoldChange` >= abs(`LFCT`)) genes...
+
+...to perform the GO enrichement analysis against all genes defined in the input file given with the `--de_file` parameter
+- `GOTYPE`: The GO term type considered in the result file:
+  - `BP`: Biological Process
+  - `MF`: Molecular Function
+  - `CC`Cellular component
+- `ALPHA`: consider genes having a `padj` <= `ALPHA` in the input file as significant
+- `LFCT`: consider genes having a
+  - `log2FoldChange` <= `LFCT` (for down-regulated genes)...
+  - `log2FoldChange` >= `LFCT` (for up-regulated genes)...
+  - `log2FoldChange` >= abs(`LFCT`) (for differentially expressed genes)...
+
+... in the input file as differentially expressed
+
+- `NUM`: The top number of enriched go term to display
+
+The pdf file corresponds to a figure displying the top enriched go terms and the text file is the same thing but in the form a tabulated file with this structure:
+
+| GO.ID      | Term                                        | Annotated | Significant | fish    |
+| ---------- | ------------------------------------------- | --------- | ----------- | ------- |
+| GO:0051240 | positive regulation of multicellular org... | 986       | 67          | 4.6e-10 |
+| GO:0010941 | regulation of cell death                    | 1206      | 76          | 8.2e-10 |
+| GO:0042127 | regulation of cell population proliferat... | 1171      | 74          | 1.3e-09 |
+
+Where:
+
+- `fish`: p-value of the GO term enrichment analysis using the Fisher method

man/build_figure.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/figure.R
+\name{build_figure}
+\alias{build_figure}
+\title{Produce figure displaying the top enriched go term}
+\usage{
+build_figure(top_go_result, go_term_type, outfile)
+}
+\arguments{
+\item{top_go_result}{dataframe containing top_go results}
+
+\item{go_term_type}{The go term type of the figure}
+
+\item{outfile}{File were the figure will be created}
+}
+\description{
+Produce figure displaying the top enriched go term
+}

man/cli_function.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/parser.R
+\name{cli_function}
+\alias{cli_function}
+\title{Parse  the command line arguments}
+\usage{
+cli_function()
+}
+\description{
+Parse the command line arguments and return an object through which all
+given arguments are stored
+}

man/cli_run_topgo.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/main.R
+\name{cli_run_topgo}
+\alias{cli_run_topgo}
+\title{Cli TopGO Wrapper}
+\usage{
+cli_run_topgo()
+}
+\description{
+Cli TopGO Wrapper
+}
+\details{
+perform a TopGO analysis using fisher statistics on human go term
+for:
+\enumerate{
+\item Each go term type: BP, MF, CC
+\item Down-regulated, Up-regulated and all differentially expressed genes
+}
+}

man/get_gene_list.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/topGO_analysis.R
+\name{get_gene_list}
+\alias{get_gene_list}
+\title{Get the gene list vector needed for differential expression}
+\usage{
+get_gene_list(de_table, regulation, alpha, log2fc_threshold)
+}
+\arguments{
+\item{de_table}{tibble containing DESeq2 enrichment score}
+
+\item{regulation}{The regulation of the gene of interest 'down', 'up' 'all'
+where 'down to perform enrichment for down-regulated genes, 'up'
+to perform enrichement for up-regulated genes and 'all' to perform
+enrichment for all differentially expressed genes}
+
+\item{alpha}{The padj threshold of a genes to be considered a significant}
+
+\item{log2fc_threshold}{The threshold above which we want to consider
+de-genes. It must be positive}
+}
+\value{
+the named vector used to build the topGO object
+}
+\description{
+Get the gene list vector needed for differential expression
+}

man/load_input.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/load_df.R
+\name{load_input}
+\alias{load_input}
+\title{Load the file containing differentially or not expressed genes}
+\usage{
+load_input(de_file)
+}
+\arguments{
+\item{de_file}{the file containing differentially or not expressed genes}
+}
+\value{
+The loaded file with a gene column
+}
+\description{
+Load the file containing differentially or not expressed genes
+}

man/run_topgo.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/main.R
+\name{run_topgo}
+\alias{run_topgo}
+\title{Perform all go term enrchment analysis}
+\usage{
+run_topgo(de_table, output_folder, id_kind, top, alpha, log2fc_threshold)
+}
+\arguments{
+\item{de_table}{tibble containing DESeq2 enrichment score}
+
+\item{output_folder}{Folder where the results will be created}
+
+\item{id_kind}{The kind of id to use in the topGO analysis. Must correspond
+to the ids defined in gene column of de_file}
+
+\item{top}{The number of most enriched GO term to return}
+
+\item{alpha}{The padj threshold of a genes to be considered a significant}
+
+\item{log2fc_threshold}{The threshold above which we want to consider
+de-genes. It must be positive}
+}
+\value{
+The table containing the go enrichment analysis performed by topGO
+}
+\description{
+Perform all go term enrchment analysis
+}

man/top_go_analysis.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/topGO_analysis.R
+\name{top_go_analysis}
+\alias{top_go_analysis}
+\title{Perform the TopGO analysis}
+\usage{
+top_go_analysis(
+  de_table,
+  id_kind,
+  go_term_type,
+  regulation,
+  top,
+  alpha,
+  log2fc_threshold
+)
+}
+\arguments{
+\item{de_table}{tibble containing DESeq2 enrichment score}
+
+\item{id_kind}{The kind of id to use in the topGO analysis. Must correspond
+to the ids defined in gene column of de_file}
+
+\item{go_term_type}{The type of go term to use in the analysis}
+
+\item{regulation}{The regulation of the gene of interest 'down', 'up' 'all'
+where 'down to perform enrichment for down-regulated genes, 'up'
+to perform enrichement for up-regulated genes and 'all' to perform
+enrichment for all differentially expressed genes}
+
+\item{top}{The number of most enriched GO term to return}
+
+\item{alpha}{The padj threshold of a genes to be considered a significant}
+
+\item{log2fc_threshold}{The threshold above which we want to consider
+de-genes. It must be positive}
+}
+\value{
+The table containing the go enrichment analysis performed by topGO
+}
+\description{
+Perform the TopGO analysis
+}