R/TaxonomicTableGUI.R
In katrikorpela/mare: Microbiota Analysis in R Easily
Defines functions
TaxonomicTableGUI
Documented in
TaxonomicTableGUI
TaxonomicTableGUI <- function(usearch.path, refDB, annotate.reads = T,
folder.name = "", confidence.cutoff = 0) {
refDB <- system.file(paste("extdata/",refDB,sep=""),package="mare")
wd <- getwd()
tobeannotated <- paste(wd, "/", folder.name, "ProcessedReads/finalreads.fasta", sep = "")
readfile <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, "_readtable.txt", sep = ""), check.names = F)
OTU <- ""
system(paste(usearch.path, " -utax ", tobeannotated, " -db ", refDB, " -utax_cutoff ",
confidence.cutoff, " -strand both -utaxout ", wd, "/", folder.name,
"TaxonomicTables/", folder.name, OTU, "taxonomy.txt", sep = ""))
if (confidence.cutoff == 0) {
taxonomy <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "taxonomy.txt", sep = ""), header = F)[, -c(3:4)]
names(taxonomy) <- c("OTUId", "taxonomy")
taxonomy$genus <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$genus[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "g:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$family <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$family[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "f:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$order <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$order[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "o:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$class <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$class[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "c:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$phylum <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$phylum[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "p:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$genus <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, sep = "_")
taxonomy$family <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, sep = "_")
taxonomy$order <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
sep = "_")
taxonomy$class <- paste(taxonomy$phylum, taxonomy$class, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
genus_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$genus), sum)
family_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$family), sum)
order_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$order), sum)
class_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$class), sum)
phylum_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$phylum), sum)
write.table(genus_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_genus_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(family_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_family_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(order_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_order_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(class_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_class_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(phylum_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_phylum_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
#readtable <- annotated_readtable[,-c(2:7)]
taxonomy$species <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$species[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "s:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$species <- gsub("_","",taxonomy$species)
taxonomy$species <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, taxonomy$species, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
species_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$species), sum)
write.table(species_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_species_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
readtable <- annotated_readtable[,-c(2:8)]
} else {
if(grepl(pattern=".udb",x=refDB)){
taxonomy <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "taxonomy.txt", sep = ""), header = F)[, -c(2,4)]
names(taxonomy) <- c("OTUId", "taxonomy")
taxonomy$genus <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$genus[j] <- strsplit(as.character(taxonomy$taxonomy[j]),
split = ",g:")[[1]][2]
taxonomy$family <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$family[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",f:")[[1]][2], split = ",")[[1]][1]
taxonomy$order <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$order[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",o:")[[1]][2], split = "[,]")[[1]][1]
taxonomy$class <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$class[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",c:")[[1]][2], split = "[,]")[[1]][1]
taxonomy$phylum <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$phylum[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",p:")[[1]][2], split = "[,]")[[1]][1]
taxonomy$genus <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, sep = "_")
taxonomy$family <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, sep = "_")
taxonomy$order <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
sep = "_")
taxonomy$class <- paste(taxonomy$phylum, taxonomy$class, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
genus_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$genus), sum)
family_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$family), sum)
order_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$order), sum)
class_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$class), sum)
phylum_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$phylum), sum)
write.table(genus_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_genus_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(family_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_family_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(order_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_order_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(class_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_class_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(phylum_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_phylum_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
readtable <- annotated_readtable[,-c(2:7)]
} else print("RefDB must be in .udb format if confidence.cutoff is not 0!")
}
readtable$OTUId<-as.character(readtable$OTUId)
names(readtable)[1]<-"taxon"
for(i in na.omit(unique(annotated_readtable$genus))) readtable$taxon[annotated_readtable$genus==i&!is.na(annotated_readtable$genus)] <- paste(i,"read",1:nrow(annotated_readtable[annotated_readtable$genus==i&!is.na(annotated_readtable$genus),]),sep="_")
readtable <- readtable[order(readtable$taxon),]
write.table(readtable, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_annotated_read_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
library(metacoder)
gen <- genus_table
rownames(gen) <- gen$taxon
gen <- gen[,-1]
seqs <- list()
for(i in rownames(gen)){
for(h in colnames(gen)){
if(gen[i,h]>0) seqs[[paste(h,i)]]<- round(gen[i,h]/1000)
}
}
newseqs <- rep(names(seqs), seqs)
tmp <- extract_taxonomy(input=newseqs,regex = "^(.*)\\ (.*)",
key=c(id = "obs_info","class"),class_sep = "_")
heat_tree(tmp, node_size = n_obs*1000,
node_label = ifelse(name == "NA", NA, name),
node_color = n_obs*1000,
node_color_axis_label = "Number of reads per taxon",
node_color_range=c("gray90","skyblue","pink","hotpink","red","firebrick"),
initial_layout = "reingold-tilford", layout = "davidson-harel",
node_size_range=c(0.01,0.04),
overlap_avoidance = 0.5,
node_label_max=200,
node_label_size_range=c(0.01,0.015),
title="Abundance of taxa in the dataset",title_size=0.03,
output_file=paste(folder.name,"HeatTree.pdf",sep="_"))
detach(package:metacoder)
}
katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions TaxonomicTableGUI
Documented in TaxonomicTableGUI
TaxonomicTableGUI <- function(usearch.path, refDB, annotate.reads = T,
folder.name = "", confidence.cutoff = 0) {
refDB <- system.file(paste("extdata/",refDB,sep=""),package="mare")
wd <- getwd()
tobeannotated <- paste(wd, "/", folder.name, "ProcessedReads/finalreads.fasta", sep = "")
readfile <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, "_readtable.txt", sep = ""), check.names = F)
OTU <- ""
system(paste(usearch.path, " -utax ", tobeannotated, " -db ", refDB, " -utax_cutoff ",
confidence.cutoff, " -strand both -utaxout ", wd, "/", folder.name,
"TaxonomicTables/", folder.name, OTU, "taxonomy.txt", sep = ""))
if (confidence.cutoff == 0) {
taxonomy <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "taxonomy.txt", sep = ""), header = F)[, -c(3:4)]
names(taxonomy) <- c("OTUId", "taxonomy")
taxonomy$genus <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$genus[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "g:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$family <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$family[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "f:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$order <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$order[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "o:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$class <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$class[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "c:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$phylum <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$phylum[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "p:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$genus <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, sep = "_")
taxonomy$family <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, sep = "_")
taxonomy$order <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
sep = "_")
taxonomy$class <- paste(taxonomy$phylum, taxonomy$class, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
genus_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$genus), sum)
family_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$family), sum)
order_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$order), sum)
class_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$class), sum)
phylum_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$phylum), sum)
write.table(genus_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_genus_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(family_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_family_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(order_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_order_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(class_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_class_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(phylum_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_phylum_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
#readtable <- annotated_readtable[,-c(2:7)]
taxonomy$species <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$species[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = "s:")[[1]][2], split = "[(]")[[1]][1]
taxonomy$species <- gsub("_","",taxonomy$species)
taxonomy$species <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, taxonomy$species, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
species_table <- aggregate(annotated_readtable[, -c(1:8)], by = list(taxon = annotated_readtable$species), sum)
write.table(species_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_species_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
readtable <- annotated_readtable[,-c(2:8)]
} else {
if(grepl(pattern=".udb",x=refDB)){
taxonomy <- read.delim(paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "taxonomy.txt", sep = ""), header = F)[, -c(2,4)]
names(taxonomy) <- c("OTUId", "taxonomy")
taxonomy$genus <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$genus[j] <- strsplit(as.character(taxonomy$taxonomy[j]),
split = ",g:")[[1]][2]
taxonomy$family <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$family[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",f:")[[1]][2], split = ",")[[1]][1]
taxonomy$order <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$order[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",o:")[[1]][2], split = "[,]")[[1]][1]
taxonomy$class <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$class[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",c:")[[1]][2], split = "[,]")[[1]][1]
taxonomy$phylum <- "NA"
for (j in 1:nrow(taxonomy)) taxonomy$phylum[j] <- strsplit(strsplit(as.character(taxonomy$taxonomy[j]),
split = ",p:")[[1]][2], split = "[,]")[[1]][1]
taxonomy$genus <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, taxonomy$genus, sep = "_")
taxonomy$family <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
taxonomy$family, sep = "_")
taxonomy$order <- paste(taxonomy$phylum, taxonomy$class, taxonomy$order,
sep = "_")
taxonomy$class <- paste(taxonomy$phylum, taxonomy$class, sep = "_")
annotated_readtable <- merge(taxonomy, readfile, by = "OTUId", all = T)
genus_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$genus), sum)
family_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$family), sum)
order_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$order), sum)
class_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$class), sum)
phylum_table <- aggregate(annotated_readtable[, -c(1:7)], by = list(taxon = annotated_readtable$phylum), sum)
write.table(genus_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_genus_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(family_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_family_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(order_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_order_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(class_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_class_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
write.table(phylum_table, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_phylum_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
readtable <- annotated_readtable[,-c(2:7)]
} else print("RefDB must be in .udb format if confidence.cutoff is not 0!")
}
readtable$OTUId<-as.character(readtable$OTUId)
names(readtable)[1]<-"taxon"
for(i in na.omit(unique(annotated_readtable$genus))) readtable$taxon[annotated_readtable$genus==i&!is.na(annotated_readtable$genus)] <- paste(i,"read",1:nrow(annotated_readtable[annotated_readtable$genus==i&!is.na(annotated_readtable$genus),]),sep="_")
readtable <- readtable[order(readtable$taxon),]
write.table(readtable, paste(wd, "/", folder.name, "TaxonomicTables/",
folder.name, OTU, "_annotated_read_table.txt", sep = ""), quote = F, row.names = F,
sep = "\t")
library(metacoder)
gen <- genus_table
rownames(gen) <- gen$taxon
gen <- gen[,-1]
seqs <- list()
for(i in rownames(gen)){
for(h in colnames(gen)){
if(gen[i,h]>0) seqs[[paste(h,i)]]<- round(gen[i,h]/1000)
}
}
newseqs <- rep(names(seqs), seqs)
tmp <- extract_taxonomy(input=newseqs,regex = "^(.*)\\ (.*)",
key=c(id = "obs_info","class"),class_sep = "_")
heat_tree(tmp, node_size = n_obs*1000,
node_label = ifelse(name == "NA", NA, name),
node_color = n_obs*1000,
node_color_axis_label = "Number of reads per taxon",
node_color_range=c("gray90","skyblue","pink","hotpink","red","firebrick"),
initial_layout = "reingold-tilford", layout = "davidson-harel",
node_size_range=c(0.01,0.04),
overlap_avoidance = 0.5,
node_label_max=200,
node_label_size_range=c(0.01,0.015),
title="Abundance of taxa in the dataset",title_size=0.03,
output_file=paste(folder.name,"HeatTree.pdf",sep="_"))
detach(package:metacoder)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.