.filterNodes <- function(adja, nodeFilter, nodeFilterPar, layout,
degree, between, close, eigen, cluster) {
adja.alltax <- adja
if (!is.null(layout) & is.matrix(layout)) {
keep <- colnames(adja)[which(colnames(adja) %in% rownames(layout))]
} else if (nodeFilter != "none") {
if (nodeFilter == "highestConnect") {
adja.tmp <- adja
diag(adja.tmp) <- 0
conct <- Matrix::rowSums(abs(adja.tmp))
conct <- names(sort(conct))[1:nodeFilterPar]
keep <- colnames(adja)[which(colnames(adja) %in% conct)]
} else if (nodeFilter == "highestDegree") {
sel <- names(sort(degree, decreasing = TRUE)[1:nodeFilterPar])
keep <- colnames(adja)[which(colnames(adja) %in% sel)]
} else if (nodeFilter == "highestBetween") {
sel <- names(sort(between, decreasing = TRUE)[1:nodeFilterPar])
keep <- colnames(adja)[which(colnames(adja) %in% sel)]
} else if (nodeFilter == "highestClose") {
sel <- names(sort(close, decreasing = TRUE)[1:nodeFilterPar])
keep <- colnames(adja)[which(colnames(adja) %in% sel)]
} else if (nodeFilter == "highestEigen") {
sel <- names(sort(eigen, decreasing = TRUE)[1:nodeFilterPar])
keep <- colnames(adja)[which(colnames(adja) %in% sel)]
} else if (nodeFilter == "clustTaxon") {
stopifnot(all(nodeFilterPar %in% colnames(adja)))
selClust <- cluster[nodeFilterPar]
keep <- names(cluster[cluster %in% selClust])
#keep <- names(cluster) %in% selnodes
} else if (nodeFilter == "clustMin") {
clusttab <- table(cluster)
selclust <- names(clusttab[clusttab >= nodeFilterPar &
names(clusttab) != 0])
keep <- names(cluster[cluster %in% selclust])
} else if (nodeFilter == "names") {
stopifnot(all(nodeFilterPar %in% colnames(adja)))
keep <- colnames(adja)[which(colnames(adja) %in% nodeFilterPar)]
}
} else {
keep <- colnames(adja)
}
# names_alltaxa <- matrix(NA, nrow = ncol(adja.alltax1), ncol = 2)
# names_alltaxa[, 1] <- colnames(adja.alltax1)
# names_alltaxa[, 2] <- colnames(x$input$adja1)
# rownames(names_alltaxa) <- names_alltaxa[,1]
#
# unitnames <- union(colnames(adja), colnames(adja2))
# names_selected_taxa <- matrix(NA, nrow = length(unitnames), ncol = 2)
# names_selected_taxa[, 1] <- unitnames
# names_selected_taxa[, 2] <- names_alltaxa[unitnames, 2]
# rownames(names_alltaxa) <- NULL
#
# if (labelsToFile == "all") {
# write.matrix(names_alltaxa, file="taxalabels.txt")
# } else if (labelsToFile == "selected") {
# write.matrix(names_selected_taxa, file="taxalabels.txt")
# }
#
#
# colnames(names_alltaxa) <- colnames(names_selected_taxa) <- c("shortened",
# "original")
#
# taxalabels <- list(all_taxa = names_alltaxa,
# selected_taxa = names_selected_taxa)
rm(adja.alltax)
return(keep = keep)
}
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