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| Original file line number | Diff line number | Diff line change |
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| #' Prepare data for UMAP | ||
| #' @export | ||
| #' @usage prepareUmapData(longDf = NULL, taxonRank = NULL, type = "taxa", | ||
| #' taxDB = NULL, cutoff = 0) | ||
| #' @param longDf input phyloprofile file in long format | ||
| #' @param taxonRank taxonomy rank for labels (e.g. "phylum") | ||
| #' @param type type of clustering, either "taxa" (default) or "genes" | ||
| #' @param taxDB path to taxonomy database | ||
| #' @param cutoff cutoff to filter data values. Default: 0 | ||
| #' @return A dataframe in wide format | ||
| #' @author Vinh Tran tran@bio.uni-frankfurt.de | ||
| #' @examples | ||
| #' rawInput <- system.file( | ||
| #' "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE | ||
| #' ) | ||
| #' longDf <- createLongMatrix(rawInput) | ||
| #' prepareUmapData(longDf, "phylum") | ||
|
|
||
| prepareUmapData <- function( | ||
| longDf = NULL, taxonRank = NULL, type = "taxa", taxDB = NULL, cutoff = 0 | ||
| ) { | ||
| if (is.null(longDf)) stop("Input data cannot be NULL") | ||
| if (is.null(taxonRank)) stop("Taxon rank must be specified!") | ||
| FAS_F <- FAS_B <- geneID <- ncbiID <- abbrName <- fullName <- NULL | ||
| # filter and subset input df | ||
| longDfSub <- longDf %>% filter(FAS_F >= cutoff & FAS_B >= cutoff) %>% | ||
| select(geneID, ncbiID, FAS_F) | ||
| # get taxon names for input taxa based on a selected supertaxon rank | ||
| taxMatrix <- getTaxonomyMatrix(taxDB) | ||
| nameList <- getNameList(taxDB) | ||
| superTaxonDf <- taxMatrix %>% | ||
| filter(abbrName %in% longDfSub$ncbiID) %>% | ||
| select(abbrName, one_of(taxonRank)) | ||
| colnames(superTaxonDf) <- c("ncbiID", "superID") | ||
| superTaxonDf <- dplyr::left_join( | ||
| superTaxonDf, nameList, by = c("superID" = "ncbiID") | ||
| ) | ||
| # transform to wide format, add taxon names and ortholog count | ||
| if (type == "taxa") { | ||
| wideDf <- data.table::dcast( | ||
| setDT(longDfSub), ncbiID ~ geneID, value.var = c("FAS_F"), | ||
| fun.aggregate = max, fill = -1 | ||
| ) | ||
| wideDf <- dplyr::left_join( | ||
| wideDf, superTaxonDf %>% select(ncbiID, Label = fullName), | ||
| by = "ncbiID" | ||
| ) | ||
| # add count (how many seed genes each taxon has, excluding co-orthologs) | ||
| seedWithTax <- longDfSub %>% select(geneID, ncbiID) | ||
| seedWithTax <- seedWithTax[!duplicated(seedWithTax),] | ||
| countDf <- data.frame(table(seedWithTax$ncbiID)) | ||
| wideDf <- dplyr::left_join( | ||
| data.frame(wideDf), countDf, by = c("ncbiID" = "Var1") | ||
| ) | ||
| } else { | ||
| wideDf <- data.table::dcast( | ||
| setDT(longDfSub), geneID ~ ncbiID, value.var = c("FAS_F"), | ||
| fun.aggregate = max, fill = -1 | ||
| ) | ||
| wideDf$Label <- wideDf$geneID | ||
| # add count (how many taxa has orthologs for each seed gene) | ||
| seedWithTax <- longDfSub %>% select(geneID, ncbiID) | ||
| seedWithTax <- seedWithTax[!duplicated(seedWithTax),] | ||
| countDf <- data.frame(table(longDfSub$geneID)) | ||
| wideDf <- dplyr::left_join( | ||
| data.frame(wideDf), countDf, by = c("geneID" = "Var1") | ||
| ) | ||
| } | ||
| return(wideDf) | ||
| } | ||
|
|
||
| #' Perform UMAP clustering | ||
| #' @export | ||
| #' @usage umapClustering(data4umap = NULL, by = "taxa", type = "binary", | ||
| #' randomSeed = 123) | ||
| #' @param data4umap data for UMAP clustering (output from prepareUmapData) | ||
| #' @param by cluster data by "taxa" (default) or "genes" | ||
| #' @param type type of data, either "binary" (default) or "non-binary" | ||
| #' @param randomSeed random seed. Default: 123 | ||
| #' @import umap | ||
| #' @return A list contain UMAP cluster objects | ||
| #' @author Vinh Tran tran@bio.uni-frankfurt.de | ||
| #' @seealso \code{\link{prepareUmapData}} | ||
| #' @examples | ||
| #' rawInput <- system.file( | ||
| #' "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE | ||
| #' ) | ||
| #' longDf <- createLongMatrix(rawInput) | ||
| #' data4umap <- prepareUmapData(longDf, "phylum") | ||
| #' umapClustering(data4umap) | ||
|
|
||
| umapClustering <- function( | ||
| data4umap = NULL, by = "taxa", type = "binary", randomSeed = 123 | ||
| ) { | ||
| if (is.null(data4umap)) stop("Input data cannot be NULL!") | ||
| ncbiID <- Label <- Freq <- geneID <- NULL | ||
| if (by == "taxa") { | ||
| subsetDt <- subset(data4umap, select = -c(ncbiID, Label, Freq)) | ||
|
|
||
| } else { | ||
| subsetDt <- subset(data4umap, select = -c(geneID, Label, Freq)) | ||
| } | ||
| if (type == "binary") { | ||
| subsetDt[subsetDt >= 0] <- 1 | ||
| subsetDt[subsetDt < 0] <- 0 | ||
| } | ||
| df.umap <- umap(subsetDt, random_state = randomSeed, preserve.seed = TRUE) | ||
| return(df.umap) | ||
| } | ||
|
|
||
|
|
||
| #' Create UMAP cluster plot | ||
| #' @export | ||
| #' @usage createUmapPlotData(umapData = NULL, data4umap = NULL, labelNr = 5, | ||
| #' excludeTaxa = "None") | ||
| #' @param umapData data contains UMAP cluster (output from umapClustering()) | ||
| #' @param data4umap data for UMAP clustering (output from prepareUmapData()) | ||
| #' @param labelNr maximal number of labels. Default: 5 | ||
| #' @param excludeTaxa hide taxa from plot. Default: "None" | ||
| #' @importFrom utils tail | ||
| #' @return A plot as ggplot object | ||
| #' @author Vinh Tran tran@bio.uni-frankfurt.de | ||
| #' @seealso \code{\link{prepareUmapData}}, \code{\link{umapClustering}} | ||
| #' @examples | ||
| #' rawInput <- system.file( | ||
| #' "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE | ||
| #' ) | ||
| #' longDf <- createLongMatrix(rawInput) | ||
| #' data4umap <- prepareUmapData(longDf, "phylum") | ||
| #' umapData <- umapClustering(data4umap) | ||
| #' createUmapPlotData(umapData, data4umap) | ||
|
|
||
| createUmapPlotData <- function( | ||
| umapData = NULL, data4umap = NULL, labelNr = 5, excludeTaxa = "None" | ||
| ) { | ||
| if (is.null(umapData) | is.null(data4umap)) | ||
| stop("Input data cannot be NULL!") | ||
| if (length(umapData) == 0 | length(data4umap) == 0) | ||
| stop("Input data cannot be EMPTY!") | ||
|
|
||
| Label <- Freq <- NULL | ||
|
|
||
| data4umap$X <- umapData$layout[,1] | ||
| data4umap$Y <- umapData$layout[,2] | ||
| # join less freq items into "other" | ||
| maxFreqDf <- data.frame( | ||
| data4umap %>% group_by(Label) %>% summarise(max = max(Freq)) | ||
| ) | ||
| minFreq <- tail(sort(unique(maxFreqDf$max)),labelNr)[1] | ||
| keepLabel <- unique(data4umap$Label[data4umap$Freq >= minFreq]) | ||
| data4umap$Label[!(data4umap$Label %in% keepLabel)] <- "[Other]" | ||
| # exclude taxa | ||
| if (length(excludeTaxa) == 0) excludeTaxa <- c("None") | ||
| if (length(excludeTaxa) > 0 & excludeTaxa[1] != "None") { | ||
| data4umap$X[data4umap$Label %in% excludeTaxa] <- NA | ||
| data4umap$Y[data4umap$Label %in% excludeTaxa] <- NA | ||
| } | ||
| return(data4umap) | ||
| } | ||
|
|
||
|
|
||
| #' Create UMAP cluster plot | ||
| #' @export | ||
| #' @usage plotUmap(plotDf = NULL, legendPos = "right", colorPalette = "Set2", | ||
| #' transparent = 0, textSize = 12) | ||
| #' @param plotDf data for UMAP plot | ||
| #' @param legendPos position of legend. Default: "right" | ||
| #' @param colorPalette color palette. Default: "Set2" | ||
| #' @param transparent transparent level (from 0 to 1). Default: 0 | ||
| #' @param textSize size of axis and legend text. Default: 12 | ||
| #' @return A plot as ggplot object | ||
| #' @author Vinh Tran tran@bio.uni-frankfurt.de | ||
| #' @seealso \code{\link{prepareUmapData}}, \code{\link{umapClustering}}, | ||
| #' \code{\link{createUmapPlotData}} | ||
| #' @examples | ||
| #' rawInput <- system.file( | ||
| #' "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE | ||
| #' ) | ||
| #' longDf <- createLongMatrix(rawInput) | ||
| #' umapData <- prepareUmapData(longDf, "phylum") | ||
| #' data.umap <- umapClustering(umapData) | ||
| #' plotDf <- createUmapPlotData(data.umap, umapData) | ||
| #' plotUmap(plotDf) | ||
|
|
||
| plotUmap <- function( | ||
| plotDf = NULL, legendPos = "right", colorPalette = "Set2", | ||
| transparent = 0, textSize = 12 | ||
| ) { | ||
| if (is.null(plotDf)) stop("Input data cannot be NULL!") | ||
| X <- Y <- Label <- Freq <- NULL | ||
| # generate plot | ||
| plot <- ggplot(plotDf, aes(x = X, y = Y, color = Label)) + | ||
| geom_point(aes(size = Freq), alpha = 1 - transparent) + | ||
| geom_rug(alpha = 1) + | ||
| theme_minimal() + | ||
| labs(x = "", y = "") + | ||
| scale_color_brewer(palette = colorPalette) + | ||
| guides(color = guide_legend(override.aes = list(alpha = 1))) + | ||
| theme( | ||
| legend.position = legendPos, | ||
| legend.text = element_text(size = textSize), | ||
| legend.title = element_text(size = textSize), | ||
| axis.text = element_text(size = textSize), | ||
| axis.title = element_text(size = textSize), | ||
| ) | ||
| return(plot) | ||
| } |
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