From 5ced6dda408d5a9b11ba69d2f656e13c25182efa Mon Sep 17 00:00:00 2001
From: Sudarshan <sudarshanshetty9@gmail.com>
Date: Wed, 9 May 2018 17:42:13 +0200
Subject: [PATCH] Delete plot_taxa_boxplot.R

---
 man/plot_taxa_boxplot.R | 61 -----------------------------------------
 1 file changed, 61 deletions(-)
 delete mode 100644 man/plot_taxa_boxplot.R

diff --git a/man/plot_taxa_boxplot.R b/man/plot_taxa_boxplot.R
deleted file mode 100644
index 87073e0..0000000
--- a/man/plot_taxa_boxplot.R
+++ /dev/null
@@ -1,61 +0,0 @@
-#' @title Taxonomic Composition Plot boxplot
-#' @description Plot taxon abundance for samples.
-#' @param x \code{\link{phyloseq-class}} object
-#' @param taxonomic.level Merge the OTUs (for phyloseq object) into a higher taxonomic level. This has to be one from colnames(tax_table(x)).
-#' @param top.otu Top number of taxa to plot.
-#' @param VariableA Specify main variable of interest. This should be one of the variables in sample_variables(x).
-#' @param title title for the plot
-#' @param color any of the palette supported by ggpubr/RColorBrewer packages or  user specified as c("red", "blue").
-#' @return A \code{\link{ggplot}} plot object.
-#' @export
-#' @examples \dontrun{
-#'   # Example data
-#'     library(microbiomeutilities)
-#'     data("DynamicsIBD")
-#'     ps1 <- DynamicsIBD
-#'     colnames(tax_table(ps1)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species" )
-#'     pn <- plot_taxa_boxplot(ps1,
-#'     taxonomic.level = "Phylum",
-#'     top.otu = 3, VariableA = "ibd_subtype",
-#'     title = "rel plot", color = "Set2")
-#'     print(pn)
-#'
-#'           }
-#' @keywords utilities
-
-plot_taxa_boxplot <- function(x, taxonomic.level, top.otu, VariableA, title, color = NULL){
-
-  if (!is.null(x@phy_tree)){
-
-    message("For plotting purpuses the phy_tree will be removed")
-    x@phy_tree = NULL
-  }
-  else {
-
-    message("The phy_tree slot is empty, easy to make the plot")
-  }
-
-  taxic <- as.data.frame(x@tax_table);
-  otudf <- as.data.frame(otu_table(x));
-  taxic$OTU <- row.names(otudf);
-  taxmat <- as.matrix(taxic);
-  new.tax <- tax_table(taxmat);
-  tax_table(x) <- new.tax;
-
-
-  # Merge the taxa at a higher taxonomic level
-
-  if (!taxonomic.level == "OTU") {
-
-    x <- aggregate_taxa(x, taxonomic.level, top = top.otu)
-  }
-
-  x1 <- transform(x, "compositional")
-  x.df0 <- suppressWarnings(suppressMessages(phy_to_ldf(x1, transform.counts = NULL))) 
-  p <- ggboxplot(x.df0, x = taxonomic.level, y = "Abundance", fill = VariableA, palette = color)
-  p <- p + ylab("Relative Abundance") + ggtitle(title) + theme(axis.text.x = element_text(face="italic", angle = 90))
-  p <- ggpar(p, legend = "right")
-  return(p)
-}
-
-