R/bar_plot_update_manual.R

In graeberlab-ucla/MetabR: MetabR: UCLA Metabolomics QC Analysis Pipeline

#' @title Functions to assist in the current UCLA Metabolomics Pipeline.
#'
#' @description This package contains functions to assist in the current UCLA Metabolomics Quality Control and Analysis Pipeline. Called by bar_update_manual. Finalizes the a page of plots of the relative amounts of the different metabolites that are part of the specified defined pathway.
#'
#' @param a the initial ggplot object
#' @param met a data frame containing the relative amounts of the different metabolites in the experiment
#' @param Title title
#' @param axis.text.x
#' @param scales parameter passed to ggplot for the facet_wrap vertical axis scale ('free', 'fixed), from ggplot: Are scales shared across all facets (the default, "fixed"), or do they vary across rows ("free_x"), columns ("free_y"), or both rows and columns ("free").
#' @param num_cond the number of conditions in the experiment
#' @param type the type of analysis or quality control being run ('tf', '')
#'
#' @return a plot of the relative amounts of a specific metabolites that are part of the specified defined pathway (based on the 'metabolites' parameter in bar_update_manual.R)
#'
# @examples bar_plot_update_manual(a, met, Title, x, y, axis.text.x, scales='free', num_cond = n, type = "tf")
#'
#' @export
#'
bar_plot_update_manual <- function(a, met, Title, x, y, axis.text.x, scales, type = NULL, num_cond=NULL,index=NULL)
{
  # col<-c("turquoise","red","plum4","steelblue1","red4","springgreen2","slateblue2","darkgreen","lightpink1","navy","olivedrab1",
  #        "orangered","darkslateblue","lightseagreen","magenta2","royalblue","yellowgreen","lightsalmon","cyan","maroon1","indianred3","mediumseagreen",
  #        "slateblue3","hotpink","lemonchiffon1","orangered4","lightcoral","tomato")
  # if(!is.null(index))
  # {
  #   j  <- 1
  #   k <- 1
  #   extra_qc <- c("peachpuff1", "seashell1", "wheat2", "snow1")
  #   res <- vector()
  #   for( i in 1:num_cond)
  #   {
  #     if(i %in% index[[1]])
  #       res <- c(res, "yellow1")
  #     else if(i %in% index[[2]])
  #       res <- c(res, "grey45")
  #     else if (i %in% index[[4]]){
  #       res <- c(res, "darkorange1")
  #     }
  #     else if(i %in% index[[3]])
  #     {
  #       res <- c(res, extra_qc[k])
  #       k <- k + 1
  #     }
  #     else
  #     {
  #       res <- c(res, col[j])
  #       j <- j + 1
  #     }
  #   }
  #   col <- res
  # }
    col<-colors

    a + geom_bar(position="dodge", stat="identity", width=0.9) +
      geom_bar(aes(linetype=under_50_percent,color = under_50_percent, size=under_50_percent),
               position="dodge", stat="identity", width=0.9) +
      guides(linetype='none',fill=guide_legend(ncol=1)) +
      scale_size_manual(values=c(0.3,0.8), guide = 'none') +
      scale_colour_manual(values = c("black", "gray29"), guide = 'none') +
      {if (type != "tf") scale_y_continuous(labels = scales::scientific)} +
      facet_wrap( ~ Name, scales=scales) +
      theme_bw() +
      scale_linetype_manual(values=c("solid","58")) +
      labs(x=x, y=y, title=Title, fill=element_blank()) +
      theme(
        plot.title=element_text(size=20, face="bold", vjust=2),         #sets title properties
        axis.title=element_text(size=16, lineheight=20, face="bold"),   #sets theme for axis font
        axis.text=element_text(size=11, face="bold"),
        axis.text.x=axis.text.x,
        legend.title=element_text(face="bold", size=12),
        legend.text=element_text(face="bold",size=12),                  #sets legend text
        strip.text=element_text(face="bold", size=15),           #sets theme for title in facets
        panel.grid.major=element_blank()) +
      {if (type != "tf") geom_errorbar(
        aes(ymin = ifelse(Av-Std < 0, 0, Av-Std), ymax=Av+Std),
        position=position_dodge(0.9), width=.2)} +
      {if (type == "tf") geom_errorbar(
        aes(ymin = ifelse(RelAmounts_Ave-RelAmounts_Std < 0, 0, RelAmounts_Ave-RelAmounts_Std),
            ymax=RelAmounts_Ave+RelAmounts_Std),
        position=position_dodge(0.9), width=.2)} +
      scale_fill_manual(values = col)

}