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
1 answer
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")
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