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| Original file line number | Diff line number | Diff line change |
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| @@ -1,14 +1,14 @@ | ||
| Package: qiime2R | ||
| Type: Package | ||
| Title: qiime2R | ||
| Version: 0.99.13 | ||
| Version: 0.99.20 | ||
| Author: Jordan Bisanz <[email protected]> | ||
| Maintainer: Jordan Bisanz <[email protected]> | ||
| Description: Importing QIIME2 artifacts and associated data into R sessions. | ||
| License: MIT | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 6.0.1 | ||
| RoxygenNote: 7.1.0 | ||
| Suggests: knitr, rmarkdown | ||
| VignetteBuilder: knitr | ||
| biocViews: Microbiome, DataImport | ||
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@@ -20,6 +20,7 @@ Imports: | |
| phyloseq (>= 1.22.3), | ||
| Hmisc (>= 4.1-1), | ||
| yaml (>= 2.2.0), | ||
| tidyr (>= 0.8.3), | ||
| dplyr (>= 0.8.1), | ||
| stats, | ||
| utils | ||
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| #' checks if metadata is in qiime2 (.tsv) | ||
| #' | ||
| #' Checks to see if a file is in qiime2 metadata format, ie contains #q2:types line dictating the type of variable (categorical/numeric) | ||
| #' | ||
| #' @param file path to the input file, ex: file="~/data/moving_pictures/table.qza" | ||
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| #' @return TRUE/FALSE | ||
| #' | ||
| #' @examples \dontrun{metadata<-is_q2metadata("q2metadata.tsv")} | ||
| #' @export | ||
| #' | ||
| #' | ||
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| is_q2metadata <- function(file){ | ||
| suppressWarnings( | ||
| if(grepl("^#q2:types", readLines(file)[2])){return(TRUE)}else{return(FALSE)} | ||
| ) | ||
| } |
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| #' Parse an imported q2 ordination text file | ||
| #' | ||
| #' @param artifact takes an artifact containing the unparsed ordination format (result of readLines) | ||
| #' @param tmp the tmp dir for artifact | ||
| #' | ||
| #' @return a data.frame with feature IDs as row names and the columns: Kingdom, Phylum, Class, Order, Family, Genus, Species | ||
| #' | ||
| #' @examples \dontrun{ord<-parse_ordination(ordination_artifact, tmpdir)} | ||
| #' @export | ||
| #' | ||
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| parse_ordination <- function(artifact, tmp){ | ||
| if(missing(artifact)){stop("Ordination not provided.")} | ||
| if(missing(tmp)){stop("Temp directory not passed.")} | ||
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| artifact$data<-artifact$data[sapply(artifact$data, function(x) x!="")] | ||
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| for (i in 1:length(artifact$data)){ | ||
| if(grepl("^Eigvals\\t|^Proportion explained\\t|^Species\\t|^Site\\t|^Biplot\\t|^Site constraints\\t", artifact$data[i])){ | ||
| curfile=strsplit(artifact$data[i],"\t")[[1]][1] | ||
| } else { | ||
| write(artifact$data[i], paste0(tmp,"/", artifact$uuid, "/data/",curfile,".tmp"), append=TRUE) | ||
| } | ||
| } | ||
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| backup<-artifact$data | ||
| artifact$data<-list() | ||
| for (outs in list.files(paste0(tmp,"/", artifact$uuid,"/data"), full.names = TRUE, pattern = "\\.tmp")){ | ||
| NewLab<-gsub(" ", "", toTitleCase(gsub("\\.tmp", "", basename(outs)))) | ||
| artifact$data[[NewLab]]<-read.table(outs,sep='\t', header=FALSE) | ||
| if(NewLab %in% c("Eigvals","ProportionExplained")){colnames(artifact$data[[NewLab]])<-paste0("PC",1:ncol(artifact$data[[NewLab]]))} | ||
| if(NewLab %in% c("Site","SiteConstraints")){colnames(artifact$data[[NewLab]])<-c("SampleID", paste0("PC",1:(ncol(artifact$data[[NewLab]])-1)))} | ||
| if(NewLab %in% c("Species")){colnames(artifact$data[[NewLab]])<-c("FeatureID", paste0("PC",1:(ncol(artifact$data[[NewLab]])-1)))} | ||
| } | ||
| artifact$data$Vectors<-artifact$data$Site #Rename Site to Vectors so this matches up with the syntax used in the tutorials | ||
| artifact$data$Site<-NULL | ||
| return(artifact) | ||
| } |
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| #' Parse Q2 taxonomy | ||
| #' | ||
| #' @param taxonomy the imported taxonomy object (the result of read_qza() containing columns Feature.ID, Taxon, and Confidence) | ||
| #' @param tax_sep The separator between taxonomic levels. Defaults to one compatible with both GreenGenes and SILVA ("; " OR ";") | ||
| #' @param trim_extra Remove leading characters from taxonomic levels: ex: k__ or D_0__. TRUE/FALSE. default=TRUE | ||
| #' | ||
| #' @return a data.frame with feature IDs as row names and the columns: Kingdom, Phylum, Class, Order, Family, Genus, Species | ||
| #' | ||
| #' @examples \dontrun{taxonomy<-parse_taxonomy(taxonomy_artifact)} | ||
| #' @export | ||
| #' | ||
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| parse_taxonomy <- function(taxonomy, tax_sep, trim_extra){ | ||
| if(missing(taxonomy)){stop("Taxonomy Table not supplied.")} | ||
| if(missing(trim_extra)){trim_extra=TRUE} | ||
| if(missing(tax_sep)){tax_sep="; |;"} | ||
| if(sum(colnames(taxonomy)==c("Feature.ID","Taxon","Confidence"))!=3){stop("Table does not match expected format (conames(obj) are Feature.ID, Taxon, Confience)")} | ||
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| taxonomy$Confidence<-NULL | ||
| if(trim_extra){ | ||
| taxonomy$Taxon<-gsub("[kpcofgs]__","", taxonomy$Taxon) #remove leading characters from GG | ||
| taxonomy$Taxon<-gsub("D_\\d__","", taxonomy$Taxon) #remove leading characters from SILVA | ||
| } | ||
| taxonomy<-suppressWarnings(taxonomy %>% separate(Taxon, c("Kingdom","Phylum","Class","Order","Family","Genus","Species"), sep=tax_sep)) | ||
| taxonomy<-apply(taxonomy, 2, function(x) if_else(x=="", NA_character_, x)) | ||
| taxonomy<-as.data.frame(taxonomy) | ||
| rownames(taxonomy)<-taxonomy$Feature.ID | ||
| taxonomy$Feature.ID<-NULL | ||
| return(taxonomy) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,13 @@ | ||
| #' A ggplot2 theme for publication-style figures | ||
| #' | ||
| #' @examples \dontrun{ggplot(data) + theme_q2r()} | ||
| #' @export | ||
| #' | ||
| #' | ||
| #' | ||
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| theme_q2r<- function () { | ||
| theme_classic(base_size=8, base_family="Helvetica") + | ||
| theme(panel.border = element_rect(color="black", size=1, fill=NA)) + | ||
| theme(axis.line = element_blank(), strip.background = element_blank()) | ||
| } |
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| #' Generates a read manifest for importing sequencing data into qiime2 | ||
| #' | ||
| #' Scans a directory for files with matching sequencing data (default: fastq.gz) and then generates a q2 compliant manifest. | ||
| #' | ||
| #' @param outfile filename for output (default: manifest_[timestamp].txt) | ||
| #' @param directory directory containing reads | ||
| #' @param extension file extension (default: .fastq.gz) | ||
| #' @param paired are reads in paired format? TRUE/FALSE (default=FALSE) | ||
| #' @param Fwd string used to denote a forward read (default= _R1) | ||
| #' @param Rev string used to denote a reverse read (default= _R2) | ||
| #' | ||
| #' @examples \dontrun{write_q2manifest("q2manifest.txt","/yourdirhere/reads/", extension=".fastq.gz", paired=TRUE)} | ||
| #' @export | ||
| #' | ||
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| write_q2manifest<-function(outfile, directory, extension, paired){ | ||
| if(missing(outfile)){outfile<-paste0("q2manifest_", gsub(" |:","", timestamp(prefix="", suffix="")),".txt")} | ||
| if(missing(directory)){stop("Directory containing reads not provided.")} | ||
| if(missing(extension)){extension=".fastq.gz"} | ||
| if(missing(paired)){paired=FALSE} | ||
| if(missing(Fwd)){Fwd="_R1"} | ||
| if(missing(Rev)){Rev="_R2"} | ||
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| files<-list.files(reads, pattern=gsub("\\.", "\\.", extension)) | ||
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| if(!paired){ | ||
| output<-data.frame(`sample-id`=gsub(gsub("\\.", "\\.", extension), "", files), `absolute-filepath`=paste0(getwd(), "/", files), check.names = FALSE) | ||
| write.table(output, file=outfile, row.names=F, quote=F, sep="\t") | ||
| } else { | ||
| output<-data.frame(`sample-id`=gsub(gsub("\\.", "\\.", extension), "", files), file=paste0(getwd(), "/", files), check.names = FALSE) | ||
| output$Read<-case_when( | ||
| grepl(Fwd, output$file)~"forward-absolute-filepath", | ||
| grepl(Rev, output$file)~"reverse-absolute-filepath", | ||
| TRUE~"Error" | ||
| ) | ||
| if(sum(grep("Error", output$Read))==0){stop("Could not assign all reads to forward or reverse in paired mode.")} | ||
| output$`sample-id`<-gsub(Fwd, "", output$`sample-id`) | ||
| output$`sample-id`<-gsub(Rev, "", output$`sample-id`) | ||
| output<-spread(output, key=Read, value=file) | ||
| write.table(output, file=outfile, row.names=F, quote=F, sep="\t") | ||
| } | ||
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| message("Manifest written to", outfile) | ||
| } | ||
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