From dca8f0b06aa5578809e0c9d6faa99432211b9b90 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Tue, 19 Dec 2023 17:07:49 +0100
Subject: [PATCH 1/6] allow control on ranks names / prefixes
---
R/assign_fasta_fun.R | 42 ++++++++++++++++++-------------
R/assign_taxo_fun.R | 9 +++++--
R/idtaxaDB_formatting_functions.R | 14 +++++------
man/assign_taxo_fun.Rd | 8 +++++-
man/fill_tax_fun.Rd | 6 ++++-
man/idtaxa_assign_fasta_fun.Rd | 10 +++++++-
6 files changed, 58 insertions(+), 31 deletions(-)
diff --git a/R/assign_fasta_fun.R b/R/assign_fasta_fun.R
index 748f8ff..c49ea70 100644
--- a/R/assign_fasta_fun.R
+++ b/R/assign_fasta_fun.R
@@ -8,6 +8,9 @@
#' @param verbose Verbose level. (1: quiet, 3: verbal)
#' @param confidence Bootstrap threshold 0...100
#' @param returnval Boolean to return values in console or not.
+#' @param ncpu Number of cpu to use.
+#' @param prefix Vector of prefixes to use (7 ranks).
+#' @param ranks_names Taxonomy ranks names (7 ranks).
#'
#'
#' @return Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
@@ -17,7 +20,9 @@
#' @export
-idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", confidence = 50, verbose = 1, returnval = TRUE, ncpu=NULL){
+idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", confidence = 50, verbose = 1,
+ returnval = TRUE, ncpu=NULL, prefix = c("k__","p__","c__","o__","f__","g__","s__"),
+ ranks_names = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species")){
if(verbose == 3){
flog.threshold(DEBUG)
}
@@ -177,25 +182,26 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co
}
# Filling taxonomy with last assigned rank.
- colnames(taxid) <- c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species")
+ colnames(taxid) <- ranks_names
flog.info("Filling missing taxonomy ranks...")
- PREFIX = c("k__","p__","c__","o__","f__","g__","s__")
+ # PREFIX = prefix
# handling possible prefix
- noprefix_taxid = taxid[grep("k__",taxid[,1], invert = TRUE),]
- prefix_taxid = taxid[grep("k__",taxid[,1]),]
-
- if(nrow(noprefix_taxid) != 0){
- noprefix_taxid = fill_tax_fun(noprefix_taxid, prefix = FALSE)
- noprefix_taxid = as.data.frame( t(apply(noprefix_taxid, 1, function(x){ paste(PREFIX, x, sep="")})), stringAsFactors = FALSE)
- colnames(noprefix_taxid) = colnames(taxid)
- }
-
- if(nrow(prefix_taxid) != 0){
- prefix_taxid = fill_tax_fun(prefix_taxid, prefix = TRUE)
- }
- filled_taxid = rbind.data.frame(noprefix_taxid, prefix_taxid)
-
- tax.table = filled_taxid[names(dna),]
+ # noprefix_taxid = taxid[grep("k__",taxid[,1], invert = TRUE),]
+ # prefix_taxid = taxid[grep("k__",taxid[,1]),]
+
+ # if(nrow(noprefix_taxid) != 0){
+ # noprefix_taxid = fill_tax_fun(noprefix_taxid, prefix = FALSE)
+ # noprefix_taxid = as.data.frame( t(apply(noprefix_taxid, 1, function(x){ paste(PREFIX, x, sep="")})), stringAsFactors = FALSE)
+ # colnames(noprefix_taxid) = colnames(taxid)
+ # }
+
+ # if(nrow(prefix_taxid) != 0){
+ # prefix_taxid = fill_tax_fun(prefix_taxid, prefix = TRUE)
+ # }
+
+ final_taxid = fill_tax_fun(prefix_taxid, prefix = prefix)
+
+ tax.table = final_taxid[names(dna),]
flog.info('Done.')
diff --git a/R/assign_taxo_fun.R b/R/assign_taxo_fun.R
index a8db57d..a650a63 100644
--- a/R/assign_taxo_fun.R
+++ b/R/assign_taxo_fun.R
@@ -9,6 +9,8 @@
#' @param confidence Bootstrap threshold 0...100
#' @param returnval Boolean to return values in console or not.
#' @param ncpu Number of cpus to use.
+#' @param prefix Vector of prefixes to use (7 ranks).
+#' @param ranks_names Taxonomy ranks names (7 ranks).
#'
#'
#' @return Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
@@ -23,7 +25,9 @@
-assign_taxo_fun <- function(dada_res = dada_res, output = "./idtaxa/", id_db = "/PathToDB/UNITE_idtaxa.Rdata", confidence = 50, verbose = 1, returnval = TRUE, ncpu=NULL){
+assign_taxo_fun <- function(dada_res = dada_res, output = "./idtaxa/", id_db = "/PathToDB/UNITE_idtaxa.Rdata",
+ confidence = 50, verbose = 1, returnval = TRUE, ncpu=NULL, prefix = c("k__","p__","c__","o__","f__","g__","s__"),
+ ranks_names = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species")){
if(verbose == 3){
@@ -41,7 +45,8 @@ assign_taxo_fun <- function(dada_res = dada_res, output = "./idtaxa/", id_db =
if(!all( names(dna) == rownames(dada_res$otu.table) )){stop("Seq names and ASV table row names are different")}
tt2 = idtaxa_assign_fasta_fun(fasta = dna, id_db = id_db,
- output = output, confidence = confidence, verbose = verbose, returnval = returnval)
+ output = output, confidence = confidence, verbose = verbose, returnval = returnval,
+ prefix = prefix, ranks_names = ranks_names)
}
diff --git a/R/idtaxaDB_formatting_functions.R b/R/idtaxaDB_formatting_functions.R
index 9e9782a..2200562 100644
--- a/R/idtaxaDB_formatting_functions.R
+++ b/R/idtaxaDB_formatting_functions.R
@@ -11,15 +11,13 @@
#' @import DECIPHER
#' @export
-fill_tax_fun <- function(taxtable = taxtable, prefix = TRUE){
+fill_tax_fun <- function(taxtable = taxtable, prefix = c("k__","p__","c__","o__","f__","g__","s__"),
+ ranks_names = c("domain","phylum","class","order","family","genus","species")){
fill_tax_table = function(x){
- RANKS = c("domain","phylum","class","order","family","genus","species")
- if(prefix){
- PREFIX = c("k__","p__","c__","o__","f__","g__","s__")
- }else{
- PREFIX = c("","","","","","","")
- }
+ RANKS <- ranks_names
+ PREFIX <- prefix
+
TAX = x
@@ -29,7 +27,7 @@ fill_tax_fun <- function(taxtable = taxtable, prefix = TRUE){
}
for( i in 1:7){
- if(is.na(TAX[i])){
+ if(is.na(TAX[i]) | grepl("__NA$", TAX[i]) ){
if(grepl(PREFIX[i-1], TAX[i-1], ignore.case = FALSE, perl = FALSE, fixed = TRUE)){
TAX[i-1] <- sub(PREFIX[i-1],'',TAX[i-1])
}
diff --git a/man/assign_taxo_fun.Rd b/man/assign_taxo_fun.Rd
index 16f04a9..bef9446 100644
--- a/man/assign_taxo_fun.Rd
+++ b/man/assign_taxo_fun.Rd
@@ -11,7 +11,9 @@ assign_taxo_fun(
confidence = 50,
verbose = 1,
returnval = TRUE,
- ncpu = NULL
+ ncpu = NULL,
+ prefix = c("k__", "p__", "c__", "o__", "f__", "g__", "s__"),
+ ranks_names = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species")
)
}
\arguments{
@@ -28,6 +30,10 @@ assign_taxo_fun(
\item{returnval}{Boolean to return values in console or not.}
\item{ncpu}{Number of cpus to use.}
+
+\item{prefix}{Vector of prefixes to use (7 ranks).}
+
+\item{ranks_names}{Taxonomy ranks names (7 ranks).}
}
\value{
Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
diff --git a/man/fill_tax_fun.Rd b/man/fill_tax_fun.Rd
index b1b32ad..c078bca 100644
--- a/man/fill_tax_fun.Rd
+++ b/man/fill_tax_fun.Rd
@@ -4,7 +4,11 @@
\alias{fill_tax_fun}
\title{Fill taxonomy table (idtaxa training functions)}
\usage{
-fill_tax_fun(taxtable = taxtable, prefix = TRUE)
+fill_tax_fun(
+ taxtable = taxtable,
+ prefix = c("k__", "p__", "c__", "o__", "f__", "g__", "s__"),
+ ranks_names = c("domain", "phylum", "class", "order", "family", "genus", "species")
+)
}
\arguments{
\item{taxtable}{Taxonomy table in tabulated format.}
diff --git a/man/idtaxa_assign_fasta_fun.Rd b/man/idtaxa_assign_fasta_fun.Rd
index 53e07c7..5f4afeb 100644
--- a/man/idtaxa_assign_fasta_fun.Rd
+++ b/man/idtaxa_assign_fasta_fun.Rd
@@ -11,7 +11,9 @@ idtaxa_assign_fasta_fun(
confidence = 50,
verbose = 1,
returnval = TRUE,
- ncpu = NULL
+ ncpu = NULL,
+ prefix = c("k__", "p__", "c__", "o__", "f__", "g__", "s__"),
+ ranks_names = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species")
)
}
\arguments{
@@ -26,6 +28,12 @@ idtaxa_assign_fasta_fun(
\item{verbose}{Verbose level. (1: quiet, 3: verbal)}
\item{returnval}{Boolean to return values in console or not.}
+
+\item{ncpu}{Number of cpu to use.}
+
+\item{prefix}{Vector of prefixes to use (7 ranks).}
+
+\item{ranks_names}{Taxonomy ranks names (7 ranks).}
}
\value{
Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
--
GitLab
From 5bbee272a3a68dc4475621d5a28dd721034a1ae2 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Thu, 21 Dec 2023 17:25:20 +0100
Subject: [PATCH 2/6] update
---
R/assign_fasta_fun.R | 2 +-
R/idtaxaDB_formatting_functions.R | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/R/assign_fasta_fun.R b/R/assign_fasta_fun.R
index c49ea70..ff6cf06 100644
--- a/R/assign_fasta_fun.R
+++ b/R/assign_fasta_fun.R
@@ -199,7 +199,7 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co
# prefix_taxid = fill_tax_fun(prefix_taxid, prefix = TRUE)
# }
- final_taxid = fill_tax_fun(prefix_taxid, prefix = prefix)
+ final_taxid = fill_tax_fun(taxid, prefix = prefix, ranks_names = ranks_names)
tax.table = final_taxid[names(dna),]
diff --git a/R/idtaxaDB_formatting_functions.R b/R/idtaxaDB_formatting_functions.R
index 2200562..7900dce 100644
--- a/R/idtaxaDB_formatting_functions.R
+++ b/R/idtaxaDB_formatting_functions.R
@@ -12,7 +12,7 @@
#' @export
fill_tax_fun <- function(taxtable = taxtable, prefix = c("k__","p__","c__","o__","f__","g__","s__"),
- ranks_names = c("domain","phylum","class","order","family","genus","species")){
+ ranks_names = c("Domain","Phylum","Class","Order","Family","Genus","Species")){
fill_tax_table = function(x){
RANKS <- ranks_names
@@ -41,7 +41,7 @@ fill_tax_fun <- function(taxtable = taxtable, prefix = c("k__","p__","c__","o__"
filltable <- tt2 <- as.data.frame( t(apply(taxtable, 1, fill_tax_table)) ,stringsAsFactors = FALSE )
- names(filltable) = c("Domain","Phylum","Class","Order","Family","Genus","Species")
+ names(filltable) = ranks_names
rownames(filltable) = rownames(taxtable)
return(filltable)
--
GitLab
From 619aa1a5acc68132dc1257db070217cc64e08e78 Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Tue, 9 Jan 2024 15:36:20 +0100
Subject: [PATCH 3/6] update
---
R/assign_fasta_fun.R | 6 +++---
R/idtaxaDB_formatting_functions.R | 17 ++++++++++++-----
man/check_tax_fun.Rd | 1 +
man/fill_tax_fun.Rd | 6 ++++--
4 files changed, 20 insertions(+), 10 deletions(-)
diff --git a/R/assign_fasta_fun.R b/R/assign_fasta_fun.R
index ff6cf06..0f0ccef 100644
--- a/R/assign_fasta_fun.R
+++ b/R/assign_fasta_fun.R
@@ -145,11 +145,11 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co
}else{
# One DB assignment
taxid <- sapply(taxid_list[[1]], function(x) {
- taxa <- rep(NA,7)
+ taxa <- rep(NA,length(ranks_names))
assign <- x$taxon
# print(assign)
if(length(assign[-1])==0){
- taxa <- rep("unassigned",7)
+ taxa <- rep("unassigned",length(ranks_names))
} else {
taxa[1:length(assign[-1])] <- assign[-1]
}
@@ -206,7 +206,7 @@ idtaxa_assign_fasta_fun <- function(fasta, id_db, output = "./assign_fasta/", co
flog.info('Done.')
flog.info("Check taxonomy consistency...")
- tax.tablecheck = check_tax_fun(tax.table, output = NULL, rank = 6, verbose = 3)
+ tax.tablecheck = check_tax_fun(tax.table, output = NULL, rank = length(ranks_names) - 1, ranks_names = ranks_names, verbose = 3)
flog.info("Done.")
#Output table 2
diff --git a/R/idtaxaDB_formatting_functions.R b/R/idtaxaDB_formatting_functions.R
index 7900dce..8b2bf9f 100644
--- a/R/idtaxaDB_formatting_functions.R
+++ b/R/idtaxaDB_formatting_functions.R
@@ -3,7 +3,8 @@
#'
#'
#' @param taxtable Taxonomy table in tabulated format.
-#' @param prefix TRUE if there are prefix like c("k__","p__","c__","o__","f__","g__","s__")
+#' @param prefix Vector of prefixes to use like c("k__","p__","c__","o__","f__","g__","s__"), NULL if no prefix.
+#' @param ranks_names Taxonomy ranks names
#'
#' @return Return the same taxonomy without empty field, last known ranks are informed.
#'
@@ -16,7 +17,11 @@ fill_tax_fun <- function(taxtable = taxtable, prefix = c("k__","p__","c__","o__"
fill_tax_table = function(x){
RANKS <- ranks_names
- PREFIX <- prefix
+ if(is.null(prefix)){
+ PREFIX <- rep("", length(ranks_names))
+ }else{
+ PREFIX <- prefix
+ }
TAX = x
@@ -26,7 +31,7 @@ fill_tax_fun <- function(taxtable = taxtable, prefix = c("k__","p__","c__","o__"
return(fTAX)
}
- for( i in 1:7){
+ for( i in 1:length(ranks_names)){
if(is.na(TAX[i]) | grepl("__NA$", TAX[i]) ){
if(grepl(PREFIX[i-1], TAX[i-1], ignore.case = FALSE, perl = FALSE, fixed = TRUE)){
TAX[i-1] <- sub(PREFIX[i-1],'',TAX[i-1])
@@ -63,8 +68,10 @@ fill_tax_fun <- function(taxtable = taxtable, prefix = c("k__","p__","c__","o__"
-check_tax_fun <- function(taxtable = taxtable, output = NULL, rank = 7, verbose=3, returnval = TRUE){
- RANKS = c("_domain","_phylum","_class","_order","_family","_genus","_species")
+check_tax_fun <- function(taxtable = taxtable, output = NULL, rank = 7,
+ ranks_names = c("Domain","Phylum","Class","Order","Family","Genus","Species"), verbose=3, returnval = TRUE){
+ RANKS <- stringr::str_to_lower(ranks_names) %>% paste("_", ., sep = "")
+
# Check for multiple ancestors at each rank, choose first occurence for each problematic taxon
sink(paste('./check_tax_fun.log', sep=""), split = TRUE)
for(rk in rank:2){
diff --git a/man/check_tax_fun.Rd b/man/check_tax_fun.Rd
index fbd76ff..3d0cb5c 100644
--- a/man/check_tax_fun.Rd
+++ b/man/check_tax_fun.Rd
@@ -8,6 +8,7 @@ check_tax_fun(
taxtable = taxtable,
output = NULL,
rank = 7,
+ ranks_names = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
verbose = 3,
returnval = TRUE
)
diff --git a/man/fill_tax_fun.Rd b/man/fill_tax_fun.Rd
index c078bca..d468721 100644
--- a/man/fill_tax_fun.Rd
+++ b/man/fill_tax_fun.Rd
@@ -7,13 +7,15 @@
fill_tax_fun(
taxtable = taxtable,
prefix = c("k__", "p__", "c__", "o__", "f__", "g__", "s__"),
- ranks_names = c("domain", "phylum", "class", "order", "family", "genus", "species")
+ ranks_names = c("Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species")
)
}
\arguments{
\item{taxtable}{Taxonomy table in tabulated format.}
-\item{prefix}{TRUE if there are prefix like c("k__","p__","c__","o__","f__","g__","s__")}
+\item{prefix}{Vector of prefixes to use like c("k__","p__","c__","o__","f__","g__","s__"), NULL if no prefix.}
+
+\item{ranks_names}{Taxonomy ranks names}
}
\value{
Return the same taxonomy without empty field, last known ranks are informed.
--
GitLab
From 08e763e14e424b9c87b06d53d36466fc86f7118b Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Thu, 18 Jan 2024 09:56:33 +0100
Subject: [PATCH 4/6] diff analysis: resolving bugs
---
R/aggregate_fun.R | 5 ++---
R/decontam_fun.R | 6 ++++--
R/deseq2_fun.R | 9 +++++----
R/metagenomeseq_fun.R | 2 +-
4 files changed, 12 insertions(+), 10 deletions(-)
diff --git a/R/aggregate_fun.R b/R/aggregate_fun.R
index 4ba022b..67b2873 100644
--- a/R/aggregate_fun.R
+++ b/R/aggregate_fun.R
@@ -96,7 +96,7 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
mgseqT <- data.frame()
}
}
- flog.debug(pander(mgseqT, split.tables=2000))
+ flog.debug(pander::pander(mgseqT, split.tables=2000))
# print(head(mgseqT))
flog.info('Metacoder.')
if(file.exists(paste(metacoder))){
@@ -177,14 +177,13 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
}
TABfbak0 <- TABf
-
# add new columns, sumMethods, DeseqLFC, Mean Relative Abundance (TSS) condition 1 & 2
- row.names(deseqT) = deseqT[,1]
if(nrow(deseqT)==0){
TABf <- cbind(TABf, sumMethods = apply(TABf[3:5], 1, sum, na.rm=TRUE),
DESeqLFC = rep(NA, nrow(TABf)),
absDESeqLFC = rep(NA, nrow(TABf)))
}else{
+ row.names(deseqT) = deseqT[,1]
TABf <- cbind( TABf, sumMethods = apply(TABf[3:5], 1, sum, na.rm=TRUE),
DESeqLFC = deseqT[as.character(TABf[,1]),"log2FoldChange"],
absDESeqLFC = abs(deseqT[as.character(TABf[,1]),"log2FoldChange"]) )
diff --git a/R/decontam_fun.R b/R/decontam_fun.R
index b7786bd..91ed919 100644
--- a/R/decontam_fun.R
+++ b/R/decontam_fun.R
@@ -322,9 +322,11 @@ decontam_fun <- function(data = data, domain = "Bacteria", output = "./decontam_
fun <- paste("data <- subset_samples(data, ",column," %in% '",spl_identifier,"')",sep="")
eval(parse(text=fun))
}
- } else{
+ } else if(column == ""){
+ flog.info(paste0('No column to remove from metadata.'))
+ }else {
flog.error(paste0(column, ' not present in metadata.'))
- exit(1)
+ # exit(1)
}
diff --git a/R/deseq2_fun.R b/R/deseq2_fun.R
index 206f1cf..dcbf310 100644
--- a/R/deseq2_fun.R
+++ b/R/deseq2_fun.R
@@ -136,8 +136,8 @@ deseq2_fun <- function(data = data, output = "./deseq/", column1 = "", verbose =
# flog.info('DESeq2...')
# print(dseq2)
-
- dseq3 = DESeq2::DESeq(dseq2, test="Wald", fitType="parametric")
+ dseq3 = try(DESeq2::DESeq(dseq2, test="Wald", fitType="parametric"))
+ if(class(dseq3) == "try-error"){next}
flog.debug(show(dseq3))
res = results(dseq3, cooksCutoff = FALSE, contrast = c(column1,combinaisons[1,col] , combinaisons[2,col]))
@@ -187,10 +187,11 @@ deseq2_fun <- function(data = data, output = "./deseq/", column1 = "", verbose =
} else{
flog.info(paste('No significant results for comparison ',combinaisons[1,col], ' ' , combinaisons[2,col], sep=''))
- tab0 = data.frame(matrix(ncol = 14, nrow = 0))
+ headers <- c(resultsNames(dseq3)[2], colnames(res), colnames(tax_table(data)))
+ tab0 = data.frame(matrix(ncol = length(headers), nrow = 0))
# print(length(c(resultsNames(deseq)[2], colnames(res), colnames(tax_table(data)))))
# print(c(resultsNames(deseq)[2], colnames(res), colnames(tax_table(data))))
- colnames(tab0) <- c(resultsNames(dseq3)[2], colnames(res), colnames(tax_table(data)))
+ colnames(tab0) <- headers
write.table(tab0, file = paste(output,'/signtab_',column1,'_',paste(combinaisons[,col],collapse="_vs_"),'.csv',sep=''),quote=FALSE,sep="\t", row.names=FALSE)
}
diff --git a/R/metagenomeseq_fun.R b/R/metagenomeseq_fun.R
index 29a2222..c6cfcf8 100644
--- a/R/metagenomeseq_fun.R
+++ b/R/metagenomeseq_fun.R
@@ -33,7 +33,7 @@ metagenomeseq_fun <- function(data = data, output = "./metagenomeseq/", column1
if(!dir.exists(output)){
dir.create(output, recursive = TRUE)
}
- ranks <- c("Domain","Phylum","Class","Order","Family","Genus","Species")
+ ranks <- rank_names(data)
if(comp == ''){
fun <- paste('combinaisons <- combn(na.omit(unique(sample_data(data)$',column1,')),2) ',sep='')
eval(parse(text=fun))
--
GitLab
From 86299dda4faae8710445020c429a6f2b94039e1b Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Mon, 22 Jan 2024 14:44:33 +0100
Subject: [PATCH 5/6] amend DESCRIPTION
---
DESCRIPTION | 2 ++
1 file changed, 2 insertions(+)
diff --git a/DESCRIPTION b/DESCRIPTION
index e18d26a..6fdb1ea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,12 +56,14 @@ Imports:
microbiome,
mixOmics,
nlme,
+ pander,
phangorn,
phyloseq,
plotly,
psadd,
qdapTools,
ranacapa,
+ readr,
readxl,
reshape2,
scales,
--
GitLab
From 0754fe4db92a8d90fb336849e93d99afb7273edd Mon Sep 17 00:00:00 2001
From: Etienne Rifa <etienne.rifa[at]insa-toulouse.fr>
Date: Mon, 22 Jan 2024 14:59:31 +0100
Subject: [PATCH 6/6] correction
---
R/assign_fasta_fun.R | 4 ++--
R/assign_taxo_fun.R | 4 ++--
man/assign_taxo_fun.Rd | 4 ++--
man/idtaxa_assign_fasta_fun.Rd | 4 ++--
4 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/R/assign_fasta_fun.R b/R/assign_fasta_fun.R
index 0f0ccef..01867c8 100644
--- a/R/assign_fasta_fun.R
+++ b/R/assign_fasta_fun.R
@@ -9,8 +9,8 @@
#' @param confidence Bootstrap threshold 0...100
#' @param returnval Boolean to return values in console or not.
#' @param ncpu Number of cpu to use.
-#' @param prefix Vector of prefixes to use (7 ranks).
-#' @param ranks_names Taxonomy ranks names (7 ranks).
+#' @param prefix Vector of prefixes to use.
+#' @param ranks_names Taxonomy ranks names.
#'
#'
#' @return Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
diff --git a/R/assign_taxo_fun.R b/R/assign_taxo_fun.R
index a650a63..d6a84e9 100644
--- a/R/assign_taxo_fun.R
+++ b/R/assign_taxo_fun.R
@@ -9,8 +9,8 @@
#' @param confidence Bootstrap threshold 0...100
#' @param returnval Boolean to return values in console or not.
#' @param ncpu Number of cpus to use.
-#' @param prefix Vector of prefixes to use (7 ranks).
-#' @param ranks_names Taxonomy ranks names (7 ranks).
+#' @param prefix Vector of prefixes to use.
+#' @param ranks_names Taxonomy ranks names.
#'
#'
#' @return Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
diff --git a/man/assign_taxo_fun.Rd b/man/assign_taxo_fun.Rd
index bef9446..787580d 100644
--- a/man/assign_taxo_fun.Rd
+++ b/man/assign_taxo_fun.Rd
@@ -31,9 +31,9 @@ assign_taxo_fun(
\item{ncpu}{Number of cpus to use.}
-\item{prefix}{Vector of prefixes to use (7 ranks).}
+\item{prefix}{Vector of prefixes to use.}
-\item{ranks_names}{Taxonomy ranks names (7 ranks).}
+\item{ranks_names}{Taxonomy ranks names.}
}
\value{
Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
diff --git a/man/idtaxa_assign_fasta_fun.Rd b/man/idtaxa_assign_fasta_fun.Rd
index 5f4afeb..6591d18 100644
--- a/man/idtaxa_assign_fasta_fun.Rd
+++ b/man/idtaxa_assign_fasta_fun.Rd
@@ -31,9 +31,9 @@ idtaxa_assign_fasta_fun(
\item{ncpu}{Number of cpu to use.}
-\item{prefix}{Vector of prefixes to use (7 ranks).}
+\item{prefix}{Vector of prefixes to use.}
-\item{ranks_names}{Taxonomy ranks names (7 ranks).}
+\item{ranks_names}{Taxonomy ranks names.}
}
\value{
Return a taxonomy table with multiple ancestor checking and incongruence checking when more than one databases are used.
--
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