rplotphyloseq

How to remove very thin Bar Plot outline/border

I wanted to remove these lines at the edge of my bar plot. I am using the phyloseq library. Here is my code, I tried changing colour/color/col to "NA" and it is the same result. I just don't like that little thin black outline. 

library(phyloseq)
data("GlobalPatterns")
gp.ch <- subset_taxa(GlobalPatterns, Phylum == "Spirochaetes")
p <- plot_bar(gp.ch, fill = "Phylum") 
p + geom_bar(stat = "identity") + scale_fill_manual(values = cbPalette)

enter image description here

Solution

  • Your problem is in function plot_bar() from package phyloseq - inside is black color for border. You can just create your function like that with extra parameter - border_color or without it.

    plot_bar_2 <-  function (physeq, x = "Sample", y = "Abundance", fill = NULL, title = NULL, facet_grid = NULL, border_color = NA) 
{
  mdf = psmelt(physeq)
  p = ggplot(mdf, aes_string(x = x, y = y, fill = fill))
  p = p + geom_bar(stat = "identity", position = "stack",  color = border_color)
  p = p + theme(axis.text.x = element_text(angle = -90, hjust = 0))
  if (!is.null(facet_grid)) {
    p <- p + facet_grid(facet_grid)
  }
  if (!is.null(title)) {
    p <- p + ggtitle(title)
  }
  return(p)
}

    and call 

    library(phyloseq)
data("GlobalPatterns")
gp.ch <- subset_taxa(GlobalPatterns, Phylum == "Spirochaetes")
p <- plot_bar_2(gp.ch, fill = "Phylum") 
p + geom_bar(stat = "identity") + scale_fill_manual(values = cbPalette)

    or with any other border color if you want

    p <- plot_bar_2(gp.ch, fill = "Phylum", border_color = "red")