mothur output visualisation with Phyloseq: unable to order the x-axis

Question

[dpc]

Hi friends I am using phyloseq R package to visualise MOTHUR output files. I am using the following code to generate stacked barplot at the phylum level.

But I can't understand how to order the x-axis either alphabetically (controls and test) or increasing or decreasing order (when numerical). Also, I'm not clear regarding the function of "labels" and "breaks" parameter.

#There is five taxa in this dataset at the phylum level. So we only need five colors for displaying them.
phylum_colors <- c("steelblue", "red", "orange","magenta", "maroon")

#Using these five colors we can now plot the bargraph.
ggplot(mdata_phylum, aes(x = Sample, y = Abundance, fill = Phylum)) + 
  #facet_grid(time~.) +
  geom_bar(stat = "identity") +
  scale_fill_manual(values = phylum_colors) +
  scale_x_discrete(
    breaks = map$sample,
    labels = map$bodyweight, 
    drop = FALSE
  )  +
# Remove x axis title, and rotate sample lables
  theme(axis.title.x = element_blank(),
        axis.text.x=element_text(angle=90,hjust=1,vjust=0.5)) + 

 # additional stuff
  guides(fill = guide_legend(reverse = TRUE, keywidth = 1, keyheight = 1)) +  # modifying the legend
  ylab("Relative Abundance (Phyla > 1%) \n") +
  ggtitle("Phylum Composition of Mothur MiSeq SOP data per individual")

Here's first few lines of my data :

head(mdata_phylum)
       OTU    Sample  Abundance    sample    type  time bodyweight     Kingdom            Phylum
1 Otu00009 DRR046797 0.13355032 DRR046797 control early         20 k__Bacteria p__Actinobacteria
2 Otu00009 DRR046803 0.12054269 DRR046803   obese  late         45 k__Bacteria p__Actinobacteria
3 Otu00009 DRR046802 0.09081125 DRR046802   obese  late         45 k__Bacteria p__Actinobacteria
4 Otu00009 DRR046805 0.08990834 DRR046805   obese early         78 k__Bacteria p__Actinobacteria
5 Otu00009 DRR046798 0.08933365 DRR046798 control early         40 k__Bacteria p__Actinobacteria
6 Otu00009 DRR046801 0.07269419 DRR046801   obese  late         45 k__Bacteria p__Actinobacteria

Can anyone please help me?

Thanks and Regards, DC7

Answer 1

[Asaf]

You will have to order the dataframe before plotting. Take a look at this thread on SO: https://stackoverflow.com/questions/3253641/order-discrete-x-scale-by-frequency-value there are several solutions.

breaks will define where there will be a tick on the axis, it's more useful when it's continuous, labels are the labels that will displayed on those ticks (or breaks).

Another note if I may, it's best to select colors from a pre-defined palette like RColorBrewer, you can select the dark2 palette for instance using: phylum_colors <- brewer.pal(5, "Dark2")

[dpc]

so, should the label and breaks be same?

[Asaf]

breaks - the positions in your data, for instance if x is 1-9 you can have breaks at `c(1,3,5,7,9). Labels - whatever you want to write on the plot in those breaks. They are not the same (they could though)

[dpc]

ok sir. Thanks. Now I understand