Part 4 - Diversity indexes with pimba_plot

Plot your results (pimba_plot.sh)

When finished with pimba_run.sh, you will be able to generate some basic plots for your results, such as PCoA, rarefaction curves, alpha and beta diversity plots. You will need only two files that pimba_run.sh will generate and one metadata file you must provide.

Example of OTU table (otu_table.txt) generated by pimba_run.sh:

Example of OTU Tax assignment (tax_assignment.txt):

Example of Metadata file (metadata.csv):

The first column must always be “SampleID” and the second column must always be “SampleName”

Then, you can run the following command:

./pimba_plot.sh -t <otu_table> -a <tax_assignment> -m <metadata> -g <group_by>

-t <otu_table> = OTU table generated by pimba_run;
-a <tax_assignment> = Tax assignment file generated by pimba_run;
-m <metadata> = CSV file with columns “SampleID” and “SampleName”, and other attributes related to each sample;
-g <groupby> = A column from the metadata that will group the results. E.g., Description. Do not specify if one does not want to group the results.\

Example:

./pimba_plot.sh -t AllSamples_otu_table.txt -a AllSamples_otus_tax_assignments.txt -m metadados.txt -g Location

The list of plots that pimba_plot.sh will generate:

alpha_diversity_dotplot.svg
rarefaction_curve2.svg
cluster_dendogram.svg
phylum_barplots.svg
class_barplots.svg
order_barplots.svg
family_barplots.svg
genus_barplots.svg\