I am trying to make multiple stacked barplots with a phyloseq object (containing OTU, TAX, and Metadata) in which the order of taxa on the barplot stays the same, but on each graph a particular taxa is colorized while the rest are grey. I written a rough draft of code using a simple data frame, but i'm not sure how to apply this to a phyloseq object.

Here is the code i've come up with:

 ##good_phylum being the specfic taxa i want colorized
 good_phylum <- c("p__Firmicutes")
 ## pig_df contains taxa information and relative abundance
 pig_df[!(pig_df$Phylum %in% good_phylum),]$Phylum <- "OTHER"
 ##organizing color palette so Firmicutes is colored blue, the rest are grey
 colors <- rep("#0000", length(unique(pig_df$Phylum)))
 colors[match('p__Firmicutes', sort(unique(pig_df$Phylum)))] <- 'blue'

 ##Plot stacked bar plot
 ggplot2(pig_df)   geom_bar(position="stack", 
 stat="Phylum")   scale_fill_manual(values = colors)   
 theme(legend.text = element_text(size = 14))

Sample data:

structure(list(Phylum = c("p__Actinobacteria", "p__Bacteroidetes", 
"p__Firmicutes", "p__Lentisphaerae", "p__Proteobacteria", "p__Spirochaetes"
), AL.5 = c(5.54534, 44.05287, 37.01594, 0, 2.71389, 10.67196
), AL.4 = c(0, 40.61791, 29.41689, 0, 0.39118, 29.57402), AL.3 = c(0.51442, 
39.55305, 35.79623, 0, 2.79092, 21.34539), AL.2 = c(2.97639, 
53.8286, 25.08614, 0, 8.70794, 9.40094), AL.1 = c(3.35874, 39.20605, 
25.74435, 0.30047, 9.23324, 22.15715), LF.5 = c(0.40971, 3.95695, 
17.63298, 0.06856, 76.56688, 1.36492), LF.4 = c(2.7231, 12.9073, 
81.70363, 0.09188, 1.12626, 1.44782), LF.3 = c(9.58431, 7.14942, 
56.77299, 0, 20.15845, 6.33483), LF.2 = c(0.26317, 17.63049, 
27.01207, 0, 53.73687, 1.3574), LF.1 = c(5.48864, 36.46061, 41.32865, 
0, 1.71807, 15.00404)), class = "data.frame", row.names = c(NA, 
-6L))

Like i said Ive written the above to work with a simple data frame, but i would like to work this into my phyloseq workflow.

Thanks in advance!

*Edit: updated with a minimal sample data frame, and code was updated to work with said df

CodePudding user response：

Not 100% percent about your desired result, but as far as I get it one option would be:

1. Make use of a named vector of colors.
2. To get your bars colored you have to map on the fill aesthetic.
3. As you mentioned that you want to make multiple charts I would suggest to make use of a plotting function:

Note: I dropped stat="Phylum" as I wasn't able to figure out from which package this stat comes from.

library(ggplot2)


plot_phylum <- function(pig_df, good_phylum) {
  colors <- c("grey", "blue")
  names(colors) < c("FALSE", "TRUE")
  labels <- c("OTHER", good_phylum)
  names(labels) < c("FALSE", "TRUE")
  ##Plot stacked bar plot
  ggplot(pig_df, aes(x = factor(1), fill = Phylum %in% good_phylum))   
    geom_bar(position="stack")   
    scale_fill_manual(values = colors, labels = labels, name = NULL)   
    theme(legend.text = element_text(size = 14))
}
plot_phylum(pig_df, "p__Firmicutes")

plot_phylum(pig_df, "p__Bacteroidetes")