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Mtremblayfr/issue320 #384

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62660cc
nmr_annotation2d: back to version 1
lecorguille Feb 4, 2020
5386359
Back to the 1st version
Jul 11, 2025
00f46eb
Update galaxy version
Jul 11, 2025
d04418e
wrapper lint
Jul 17, 2025
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57 changes: 36 additions & 21 deletions tools/nmr_annotation2d/annotationRmn2D.R
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
##########################################################################
# ANNOTATION SPECTRE 2D MATRICE COMPLEXE BASEE SUR UNE SEQUENCE RMN #
# matriceComplexe : data.frame liste couples ppm de la matrice a annoter #
# BdDStandards : objet contenant la base de donnees des composes standards #
# nom_sequence : nom sequence 2D a utiliser pour annotation ("JRES", "COSY", "TOCSY", "HMBC", "HSQC") #
# ppm1Tol : tolerance ppm axe abscisses #
# ppm2Tol : tolerance ppm axe ordonnees #
# nb_ligne_template : preciser le nombre total de ligne de la feuille de calcul a annoter #
#######################################################################################################
###########################################################################################################################################
# ANNOTATION SPECTRE 2D MATRICE COMPLEXE BASEE SUR UNE SEQUENCE RMN #
# matriceComplexe : data.frame liste couples ppm de la matrice a annoter #
# BdDStandards : objet contenant la base de donnees des composes standards #
# nom_s�quence : nom sequence 2D a utiliser pour annotation ("JRES","COSY","TOCSY","HMBC","HSQC") #
# ppm1Tol : tolerance ppm axe abscisses #
# ppm2Tol : tolerance ppm axe ordonnees #
# nb_ligne_template : pr�ciser le nombre total de ligne de la feuille de calcul � annoter #
###########################################################################################################################################
annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol = 0.01, ppm2Tol = 0.01,
seuil = 0, unicite = "NO") {
## Longueur de la peak-list de la matrice a annoter
Expand All @@ -19,14 +19,15 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
seuil_score <- seuil

## Boucle sur les metabolites inclus dans BdD
for (i in seq_len(nbMetabolitesBdD)) {
for (i in 1:nbMetabolitesBdD)
{
## Infos metabolite en cours
iMetabolite <- BdDStandards[[i]]
ppm1M <- iMetabolite[, 1]
ppm2M <- iMetabolite[, 2]
nbPeakMetabolite <- length(ppm1M)
MetaboliteName <- names(BdDStandards[i])

## print(MetaboliteName)
## Initialisation
k <- 0
presenceScore <- 0
Expand All @@ -37,7 +38,8 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
metabolitesList <- data.frame()

## Boucle sur les couples de pics de la matrice a annoter
for (p in seq_len(PeakListLength)) {
for (p in 1:PeakListLength)
{
ppmAnnotationF1 <- as.numeric(matriceComplexe[p, 3])
ppmAnnotationF2 <- as.numeric(matriceComplexe[p, 2])
e <- simpleMessage("end of file")
Expand All @@ -52,7 +54,8 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
WhichMetaboliteIn <- which(metaboliteIn)
# Si au moins un couple de la matrice a annoter dans liste couples metabolite standard
if (length(WhichMetaboliteIn) > 0) {
for (a in seq_len(length(WhichMetaboliteIn))) {
for (a in 1:length(WhichMetaboliteIn))
{
annotatedPpmList <- data.frame(ppm1 = ppm1M[WhichMetaboliteIn[a]], ppm2 = ppm2M[WhichMetaboliteIn[a]], theoricalLength = nbPeakMetabolite)
annotatedPpmRef <- rbind(annotatedPpmRef, annotatedPpmList)
}
Expand All @@ -75,7 +78,7 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
annotatedPeakLength <- nrow(annotatedPpmRef) - sum(duplicated(annotatedPpmRef))
annotatedPpmRef <- annotatedPpmRef[-duplicated(annotatedPpmRef), ]
}
presenceScore <- round(annotatedPeakLength / nbPeakMetabolite, 2)
presenceScore <- annotatedPeakLength / nbPeakMetabolite
}

## Conservation metabolites dont score > seuil
Expand All @@ -91,6 +94,7 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
commonPpmList <- data.frame()
metaboliteAdd <- data.frame()
metaboliteAddList <- data.frame()
# metabolite_ref <- data.frame()
commonMetabolitesList <- data.frame()
commonMetabolitesPpmList <- data.frame()
commonMetabolitesPpmAllList1 <- data.frame()
Expand All @@ -100,9 +104,11 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
metabolitesAllUnicite <- data.frame()

## Boucle sur tous couples annotes
for (j in seq_len(length(allMetabolitesList$ppm1))) {
for (j in 1:length(allMetabolitesList$ppm1))
{
## Boucle sur metabolites dans BdD composes standards
for (i in seq_len(nbMetabolitesBdD)) {
for (i in 1:nbMetabolitesBdD)
{
ppmMetaboliteBdD <- BdDStandards[[i]]
ppm1M <- ppmMetaboliteBdD[, 1]
ppm2M <- ppmMetaboliteBdD[, 2]
Expand All @@ -121,6 +127,7 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
commonPpmList <- unique(commonPpmList)
metaboliteAdd <- data.frame(nom_metabolite = MetaboliteName)
metaboliteAddList <- rbind.data.frame(metaboliteAddList, metaboliteAdd)
# metabolite_ref <- data.frame(nom_metabolite=allMetabolitesList[j,3])
commonMetabolitesList <- rbind.data.frame(data.frame(nom_metabolite = allMetabolitesList[j, 3]), metaboliteAddList)
commonMetabolitesPpmList <- cbind.data.frame(commonPpm, commonMetabolitesList)
commonMetabolitesPpmAllList1 <- rbind.data.frame(commonMetabolitesPpmAllList1, commonMetabolitesPpmList)
Expand All @@ -146,7 +153,8 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
}

unicitynbCouplesRectif <- data.frame()
for (g in seq_len(nrow(unicityAllList))) {
for (g in 1:nrow(unicityAllList))
{
metaboliteUnicity <- (unicityAllList$Metabolite == unicityAllList$Metabolite[g])
WhichMetaboliteUnicity <- which(metaboliteUnicity)
nb_occurence <- length(WhichMetaboliteUnicity)
Expand All @@ -159,15 +167,18 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
unicityAllList <- unicityAllList[, -3]
unicityAllList <- unicityAllList[, -4]

## unicityAllList <- filter(unicityAllList, unicityAllList$score_unicite > seuil_score)
unicityAllList <- unicityAllList[unicityAllList$score_unicite > seuil_score, ]

listeTotale_metabo <- data.frame()
if (nrow(commonPpmList) != 0) {
for (o in seq_len(length(commonPpmList[, 1]))) {
for (o in 1:length(commonPpmList[, 1]))
{
tf6 <- (commonMetabolitesPpmAllList$ppm1 == commonPpmList[o, 1] & commonMetabolitesPpmAllList$ppm2 == commonPpmList[o, 2])
w6 <- which(tf6)

for (s in seq_len(length(w6))) {
for (s in 1:length(w6))
{
metaboliteAdd <- data.frame(nom_metabolite = commonMetabolitesPpmAllList[w6[s], 3])
commonMetabolitesList <- paste(commonMetabolitesList, metaboliteAdd[1, ], sep = " ")
}
Expand Down Expand Up @@ -214,13 +225,17 @@ annotationRmn2D <- function(matriceComplexe, BdDStandards, nom_sequence, ppm1Tol
scale_y_reverse(breaks = seq(maxY, 0, indice_negatif)) +
xlab("1H chemical shift (ppm)") + ylab(paste(atome, " chemical shift (ppm)")) + ggtitle(nom_sequence) +
geom_text(
data = listeTotale_2D_a_utiliser, aes(d1.ppm, d2.ppm, label = str_to_lower(substr(listeTotale_2D_a_utiliser[, 3], 1, 3)), col = probability.score),
data = listeTotale_2D_a_utiliser, aes(d1.ppm, d2.ppm,
label = str_to_lower(substr(listeTotale_2D_a_utiliser[, 3], 1, 3)),
col = probability.score
),
size = 4, hjust = 0, nudge_x = 0.02, vjust = 0, nudge_y = 0.2
) + scale_colour_manual(values = viridis(lgr))
## scale_color_colormap('Annotation', discrete=T, reverse=T)
print(sp)
}

# Liste des resultats (couples pmm / metabolite / score) + liste ppms metabolites communs
# Liste des r�sultats (couples pmm / metabolite / score) + liste ppms metabolites communs
if (unicite == "NO") {
return(list(liste_resultat = allMetabolitesList, listing_ppm_commun = listeTotale_metabo))
} else {
Expand Down
2 changes: 1 addition & 1 deletion tools/nmr_annotation2d/annotationRmn2D.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0+galaxy3" profile="20.09">
<tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0+galaxy4" profile="20.09">
<description>Annotation of complex mixture bidimensional NMR spectra</description>

<requirements>
Expand Down
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