Generating Taxonomy Summaries

This document describes how to perform taxonomy summaries for samples or for categories from a users mapping file. We will also illustrate the use of a sorting script that will allow users to sort their OTU table, so the charts will represent that order.

Here we will illustrate how to generate summarized taxonomy charts using the QIIME tutorial dataset.

Step 1. Sort OTU Table by Category in Mapping File (Optional)

Users can sort their OTU table using the mapping file and sort_otu_table.py script

sort_otu_table.py -i seqs_otu_table.txt -o seqs_otu_table_sorted_by_DOB.txt -m Fasting_Map.txt -s DOB

The resulting OTU Table will look something like the following, where the samples are sorted by the mouse date of birth:

#OTU ID PC.356  PC.354  PC.355  PC.481  PC.607  PC.593  PC.634  PC.635  PC.636  Consensus Lineage
0       0       0       0       0       0       0       0       1       0       Root;Bacteria;Firmicutes;"Clostridia";Clostridiales;"Lachnospiraceae"
1       0       0       0       0       1       0       0       0       0       Root;Bacteria;Firmicutes;"Clostridia";Clostridiales;"Lachnospiraceae"

where 0 and 1 are OTU ids, and PC.* are sample ids.

Step 2. Summarize OTU Table by Mapping Category (Optional)

Users can summarize their OTU table using one of the column headers in the mapping file and summarize_otu_by_cat.py script.

Note

• If the user performed Step 1, then this script will override the OTU table order, since it is combining samples into the category defined.

summarize_otu_by_cat.py -i Fasting_Map.txt -c seqs_otu_table.txt -m Treatment

The resulting OTU Table (Treatment_otu_table.txt) will have category ids instead of sample ids as shown below.

Note

• The categories are sorted by the order they are listed in your mapping file:

#Category OTU Counts-Treatment
#OTU ID Fast    Control Consensus Lineage
0       1       0       Root; Bacteria; Firmicutes; "Clostridia"; Clostridiales; "Lachnospiraceae"
1       1       0       Root; Bacteria; Firmicutes; "Clostridia"; Clostridiales; "Lachnospiraceae"

where 0 and 1 are OTU ids, and Fast/Control are the category ids.

Step 3. Summarize Taxa in OTU Table

For summarizing the taxa, the following will illustrate the usage based on whether the user performed either Steps 1, 2 or neither, where the user can use the summarize_taxa.py script. For each of the following examples, we will summarize the taxa at the Phylum level (3).

Example 1: case where the user did not perform Steps 1 or 2.

summarize_taxa.py -L 3 -i seqs_otu_table.txt -o seqs_otu_table_summarized.txt

The resulting summarized taxa will look something like:

Taxon       PC.354  PC.355  PC.356  PC.481  PC.593  PC.607  PC.634  PC.635  PC.636
Root;Bacteria;Actinobacteria        0.0     0.0     0.0     0.00684931506849        0.0     0.0134228187919 0.02    0.00675675675676        0.00680272108844
Root;Bacteria;Bacteroidetes 0.0472972972973 0.267123287671  0.1     0.130136986301  0.214765100671  0.275167785235  0.646666666667  0.47972972973   0.65306122449

where Root;Bacteria;* are Taxa, and PC.* are the sample ids.

Example 2: case where the user performed Step 1.

summarize_taxa.py -L 3 -i seqs_otu_table_sorted_by_DOB.txt -o seqs_otu_table_sorted_by_DOB_summarized.txt

The resulting summarized taxa will look something like:

Taxon       PC.356  PC.354  PC.355  PC.481  PC.607  PC.593  PC.634  PC.635  PC.636
Root;Bacteria;Actinobacteria        0.0     0.0     0.0     0.00684931506849        0.0134228187919 0.0     0.02    0.00675675675676        0.00680272108844
Root;Bacteria;Bacteroidetes 0.1     0.0472972972973 0.267123287671  0.130136986301  0.275167785235  0.214765100671  0.646666666667  0.47972972973   0.65306122449

where Root;Bacteria;* are Taxa, and PC.* are the category ids, but note that the order of the sample ids are based on the DOB category in the mapping file.

Example 3: case where the user performed Step 2.

summarize_taxa.py -L 3 -i Treatment_otu_table.txt -o Treatment_otu_table_summarized.txt

The resulting summarized taxa will look something like:

Taxon       Fast    Control
Root;Bacteria;Actinobacteria        0.0117845117845 0.00135317997294
Root;Bacteria;Bacteroidetes 0.513468013468  0.151556156969

where Root;Bacteria;* are Taxa, and Fast/Control are the category ids.

Step 4. Generate the Summarized Taxa Charts

Now that the user has summarized the taxa, they can generate area, bar or pie charts for their data using plot_taxa_summary.py. Here we will generate bar charts with a white background for each example from the previous step:

Example 1: case where the user did not perform Steps 1 or 2.

plot_taxa_summary.py -i seqs_otu_table_summarized.txt -l Phylum -o bar_charts -c bar -k white

The resulting plot should look like the following:

Example 2: case where the user performed Step 1.

plot_taxa_summary.py -i seqs_otu_table_summarized.txt -l Phylum -o bar_charts -c bar -k white

The resulting plot should look like the following and notice that PC.356 is now the first sample based on the sorting of sample ids from Step 1:

Example 3: case where the user performed Step 2.

plot_taxa_summary.py -i seqs_otu_table_summarized.txt -l Phylum -o bar_charts -c bar -k white

The resulting plot should look like the following: