biom_calc module¶

This module provides methods for calculating various metrics with regards to each OTU in an input OTU abundance table.

arcsine_sqrt_transform¶

Takes the proportion data from relative_abundance() and applies the variance stabilizing arcsine square root transformation:

$X = sin^{-1} (\sqrt (p))$

usage: phylotoast.biom_calc.arcsine_sqrt_transform(rel_abd)

rel_abd:¶: Refers to a dictionary keyed on SampleIDs, and the values are dictionaries keyed on OTUID’s and their values represent the relative abundance of that OTUID in that SampleID. rel_abd is the output of relative_abundance() function.

return:¶: Returns a dictionary keyed on SampleIDs, and the values are dictionaries keyed on OTUID’s and their values represent the transformed relative abundance of that OTUID in that SampleID.

Calculate the mean OTU abundance percentage.

usage: phylotoast.biom_calc.mean_otu_pct_abundance(rel_abd, otuIDs)

rel_abd:¶: Refers to a dictionary keyed on SampleIDs, and the values are dictionaries keyed on OTUID’s and their values represent the relative abundance of that OTUID in that SampleID. rel_abd is the output of relative_abundance() function.

otuIDs:¶: A list of OTUID’s for which the percentage abundance needs to be measured.

return:¶: A dictionary of OTUID and their percent relative abundance as key/value pair.

Calculate the mean relative abundance.

usage: phylotoast.biom_calc.MRA(biomf)

return:¶: A dictionary keyed on OTUID’s and their mean relative abundance for a given number of sampleIDs.

Calculate the total number of sequences in each OTU or SampleID.

usage: phylotoast.biom_calc.raw_abundance(biomf, sampleIDs=None, sample_abd=True)

sampleIDs:¶: A list of column id’s from BIOM format OTU table. By default, the list has been set to None.

sample_abd:¶: A boolean operator to provide output for OTUID’s or SampleID’s. By default, the output will be provided for SampleID’s.

return:¶: Returns a dictionary keyed on either OTUID’s or SampleIDs and their respective abundance as values.

Calculate the relative abundance of each OTUID in a Sample.

usage: phylotoast.biom_calc.relative_abundance(biomf)

return:¶: Returns a dictionary keyed on SampleIDs, and the values are dictionaries keyed on OTUID’s and their values represent the relative abundance of that OTUID in that SampleID.

Function to transform the total abundance calculation for each sample ID to another format based on user given transformation function.

usage: phylotoast.biom_calc.transform_raw_abundance(biomf, fn=math.log10, sampleIDs=None, sample_abd=True)

fn:¶: Mathematical function which is used to transform smax to another format. By default, the function has been given as base 10 logarithm.

sampleIDs:¶: A list of column id’s from BIOM format OTU table. By default, the list has been set to None.

sample_abd:¶: A boolean operator to provide output for OTUID’s or SampleID’s. By default, the output will be provided for SampleID’s.

return:¶: Returns a dictionary similar to output of raw_abundance function but with the abundance values modified by the mathematical operation. By default, the operation performed on the abundances is base 10 logarithm.