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Barplot (version 0.11.1.1)

HUMAnN2 table with optional metadata:

Feature ID of interest (give ID not full name):

Number of top stratifications to highlight:

top = highest grand means

Sample sorting methods:

Metadatum to highlight / group by:

End of metadata rows:

Color space for stratifications:

Color space for metadata levels:

Do not include the 'unclassified' stratum?:

Scaling options for total bar heights:

Strata are always proportional to height

Collapse species to genera?:

Add y-axis grid?:

Do not plot samples with zero sum for this feature?:

Image width in inches:

Image height in inches:

Limits of y-axis (2 floats separated with a space):

Format for the output:

What it does

HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.

Read more about the tool: http://huttenhower.sph.harvard.edu/humann2/manual.

humann2_barplot produces plots of stratified HUMAnN2 features and includes many options for sorting and scaling data

Here is an example of a HUMAnN2 barplot for a pathway (denitrification) that was preferentially enriched in Human Microbiome Project oral samples relative to other body sites. This figure uses many options from humann2_barplot, including regrouping by genus, pseudolog scaling, and sorting samples by similarity and metadata:

/repository/static/images/11d7b33ca2eca297/731303924-page_DENITRIFICATION-PWY.png