diff --git a/DESCRIPTION b/DESCRIPTION
index 6fdb1eab80f2204de67b08110faf408f49d48f95..0bcdc97fa5e4c456a19c637cde46e0f911c2c73c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,18 +1,9 @@
Package: ranomaly
Title: An R package grouping ANOMALY worflow functions
Version: 1.0.0
-Author@R:
- c(person(given = "Sebastien",
- family = "Theil",
- role = c("aut", "cre"),
- email = "sebastien.theil@inrae.fr"),
- person(given = "Etienne",
- family = "Rifa",
- role = "aut",
- email = "etienne.rifa@inrae.fr"))
-Author: Sebastien Theil [aut, cre],
- Etienne Rifa [aut]
-Maintainer: Sebastien Theil <sebastien.theil@inrae.fr>, Etienne Rifa <etienne.rifa@inrae.fr>
+Author: Sebastien Theil [aut, cre], Etienne Rifa [aut]
+Maintainer: Sebastien Theil <sebastien.theil@inrae.fr>, Etienne Rifa
+ <etienne.rifa@inrae.fr>
Description: rANOMALY use Amplicon Sequence Variant (ASV from Dada2
package) as taxonomic unit, allowing an easy and relevant sequence
tracking between different environments and/or projects. Decontam
@@ -33,6 +24,7 @@ Imports:
BiocGenerics,
Biostrings,
cluster,
+ ComplexHeatmap,
dada2,
DECIPHER,
decontam,
@@ -83,7 +75,10 @@ Remotes:
github::grunwaldlab/metacoder,
github::mikelove/DESeq2,
github::mixOmicsTeam/mixOmics
+Author@R: c(person(given = "Sebastien", family = "Theil", role = c("aut",
+ "cre"), email = "sebastien.theil@inrae.fr"), person(given = "Etienne",
+ family = "Rifa", role = "aut", email = "etienne.rifa@inrae.fr"))
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NAMESPACE b/NAMESPACE
index ee9b190ce48213f52a426cd3a8d906283608bb8d..fbf7f3873512c29108c839362d647651aeb3dfaa 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -18,6 +18,7 @@ export(export_to_stamp_fun)
export(fill_tax_fun)
export(generate_phyloseq_fun)
export(generate_tree_fun)
+export(heatmapDeseq2_fun)
export(heatmap_fun)
export(idTaxa_assign)
export(idtaxa_assign_fasta_fun)
@@ -55,6 +56,7 @@ import(readr)
import(readxl)
import(reshape2)
import(scales)
+import(stringr)
import(tools)
import(vegan)
import(vroom)
@@ -62,6 +64,7 @@ importFrom(Biobase,AnnotatedDataFrame)
importFrom(Biobase,fData)
importFrom(BiocGenerics,estimateSizeFactors)
importFrom(Biostrings,DNAStringSet)
+importFrom(ComplexHeatmap,pheatmap)
importFrom(DECIPHER,AlignSeqs)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,results)
diff --git a/R/heatmapDeseq2_fun.R b/R/heatmapDeseq2_fun.R
new file mode 100644
index 0000000000000000000000000000000000000000..e5d3cd0cc551fe968ea8bbad420bf8ceeddb167a
--- /dev/null
+++ b/R/heatmapDeseq2_fun.R
@@ -0,0 +1,108 @@
+#' heatmap for deseq2_fun output
+#'
+#' @param desq output of deseq2_fun
+#' @param phys the phyloseq object used for deseq2 analyse
+#' @param var Factor to test.
+#' @param workingRank Taxonomy rank used in deseq2_fun function.
+#' @param output Output directory
+#' @return Return a list object with heatmap plots and data matrix.
+#' @import futile.logger
+#' @import stringr
+#' @import phyloseq
+#' @importFrom ComplexHeatmap pheatmap
+#' @export
+
+heatmapDeseq2_fun <- function(desq, phys, var, workingRank, output = "./deseq/heatmap/") {
+ dir.create(output, recursive = TRUE)
+ PList = list()
+ for (i in names(desq)) {
+ PList[[i]] <- heatmapDeseq2_funSub(desq[[i]], phys, var, workingRank, i)
+ png(glue::glue("{output}/pheatmap-{i}.png"), width = 1200, height = 800, res = 150)
+ print(glue::glue("Output {i}"))
+ print(PList[[i]])
+ dev.off()
+ }
+ return(PList)
+}
+
+#' heatmap for deseq2_fun output
+#'
+#' @param desq output of deseq2_fun
+#' @param phys the phyloseq object used for deseq2 analyse
+#' @param var Factor to test.
+#' @param workingRank Taxonomy rank used in deseq2_fun function.
+#' @param i deseq subset name
+#' @return Return a list object with heatmap plots.
+#' @import futile.logger
+#' @import stringr
+#' @import phyloseq
+#' @importFrom ComplexHeatmap pheatmap
+
+heatmapDeseq2_funSub <- function(desq, phys, var, workingRank, i) {
+ tableDESeqSig <- desq[["table"]] |> subset(padj < 0.05) |> na.omit()
+
+ # remove unused taxa
+ psTaxaRelSig <- prune_taxa(row.names(tableDESeqSig),
+ transform_sample_counts(phys, function(x) x/sum(x)))
+
+ # remove unused sample
+ keepSamp <<- stringr::str_split(i, "_vs_", simplify = TRUE)
+
+ psTaxaRelSig2 <- paste("psTaxaRelSigSubset <<- subset_samples(psTaxaRelSig, ",
+ var, " %in% keepSamp)", sep = "")
+ eval(parse(text = psTaxaRelSig2))
+ psTaxaRelSigSubset <- subset_taxa(psTaxaRelSigSubset,
+ taxa_sums(psTaxaRelSigSubset) != 0)
+ pmatrix <- otu_table(psTaxaRelSigSubset) |>
+ data.frame() |>
+ as.matrix()
+ if (!taxa_are_rows(psTaxaRelSigSubset)) {
+ colnames(pmatrix) <- tax_table(psTaxaRelSigSubset)[, workingRank] |>
+ as.character()
+ } else {
+ rownames(pmatrix) <- tax_table(psTaxaRelSigSubset)[, workingRank] |>
+ as.character()
+ }
+
+ metadataSub <- sample_data(psTaxaRelSigSubset) |>
+ data.frame()
+ # print(metadataSub)
+
+ if (length(var) == 1) {
+ annotationCol <- data.frame(
+ var1 = metadataSub[, var[1]] |>
+ as.vector() |>
+ as.factor(),
+ check.names = FALSE)
+ } else {
+ annotationCol <- data.frame(
+ var1 = metadataSub[, var[1]] |>
+ as.vector() |>
+ as.factor(),
+ var2 = metadataSub[, var[2]] |>
+ as.vector() |>
+ as.factor(),
+ check.names = FALSE)
+ }
+
+ rownames(annotationCol) <- rownames(metadataSub)
+ colnames(annotationCol) <- var
+
+ annotationRow <- data.frame(
+ Phylum = tax_table(psTaxaRelSigSubset)[, "Phylum"] |>
+ as.factor()
+ )
+ if (taxa_are_rows(psTaxaRelSigSubset)) {
+ rownames(annotationRow) <- rownames(pmatrix)
+ } else {
+ rownames(annotationRow) <- colnames(pmatrix)
+ }
+ title <- i
+
+ pheat <- ComplexHeatmap::pheatmap(pmatrix, scale = "row",
+ annotation_col = annotationCol,
+ annotation_row = annotationRow,
+ main = title)
+
+ return(list(pheat=pheat,pmatrix=pmatrix))
+}
diff --git a/man/heatmapDeseq2_fun.Rd b/man/heatmapDeseq2_fun.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..333bd8b68bc6f901b7fd8563da90b46a5ed5a028
--- /dev/null
+++ b/man/heatmapDeseq2_fun.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/heatmapDeseq2_fun.R
+\name{heatmapDeseq2_fun}
+\alias{heatmapDeseq2_fun}
+\title{heatmap for deseq2_fun output}
+\usage{
+heatmapDeseq2_fun(desq, phys, var, workingRank, output = "./deseq/heatmap/")
+}
+\arguments{
+\item{desq}{output of deseq2_fun}
+
+\item{phys}{the phyloseq object used for deseq2 analyse}
+
+\item{var}{Factor to test.}
+
+\item{workingRank}{Taxonomy rank used in deseq2_fun function.}
+
+\item{output}{Output directory}
+}
+\value{
+Return a list object with heatmap plots and data matrix.
+}
+\description{
+heatmap for deseq2_fun output
+}
diff --git a/man/heatmapDeseq2_funSub.Rd b/man/heatmapDeseq2_funSub.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..dc347fd8b5719a8650f6eff61bfd0dcc778d5d90
--- /dev/null
+++ b/man/heatmapDeseq2_funSub.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/heatmapDeseq2_fun.R
+\name{heatmapDeseq2_funSub}
+\alias{heatmapDeseq2_funSub}
+\title{heatmap for deseq2_fun output}
+\usage{
+heatmapDeseq2_funSub(desq, phys, var, workingRank, i)
+}
+\arguments{
+\item{desq}{output of deseq2_fun}
+
+\item{phys}{the phyloseq object used for deseq2 analyse}
+
+\item{var}{Factor to test.}
+
+\item{workingRank}{Taxonomy rank used in deseq2_fun function.}
+
+\item{i}{deseq subset name}
+}
+\value{
+Return a list object with heatmap plots.
+}
+\description{
+heatmap for deseq2_fun output
+}