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Export to GraPhlAn (version 0.19)

Input file:

Identical to LEfSe input file (--lefse_input)

Use a LEfSe output file as input?:

List which levels should be annotated in the tree (Optional):

The levels must be in comma-separated form (--annotations)

List which levels should use the external legend for the annotation (Optional):

The levels must be in comma-separated form (--external_annotations)

List which levels should be highlight with a shaded background (Optional):

The levels must be in comma-separated form (--background_levels)

List of the clades that should be highlight with a shaded background (Optional):

The clades must be in comma-separated form (--background_clades)

List of color to use for the shaded background (Optional):

Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form (--background_colors)

Title of the GraPhlAn plot (Optional):

(--title)

Title font size:

(--title_font_size)

Default size for clades that are not found as biomarkers:

(--def_clade_size)

Minimum value of clades that are biomarkers:

(--min_clade_size)

Maximum value of clades that are biomarkers:

(--max_clade_size)

Default font size:

(--def_font_size)

Minimum font size:

(--min_font_size)

Maximum font size:

(--max_font_size)

Font size for the annotation legend:

(--annotation_legend_font_size)

Minimun abundance value for a clade to be annotated:

(--abundance_threshold)

Number of clades to highlight (Optional):

(--most_abundant)

Minimum number of biomarkers to extract (Optional):

The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)

Row number containing the names of the features:

-1 specifies that no names are present in the matrix (--fname_row)

Row number containing the names of the samples:

-1 specifies that no names are present in the matrix (--sname_row)

Row number to use as metadata (Optional):

(--metadata_rows)

Row number to skip from the input file:

The row numbers ar indexed to 0 and comma separated (--skip_rows)

Percentile of sample value distribution for sample selection (Optional):

(--sperc)

Percentile of feature value distribution for sample selection (Optional):

(--fperc)

Number of top samples to select (Optional):

The order is based on percentile specified by --sperc (--stop)

Number of top features to select (Optional):

The order is based on percentile specified by --fperc (--ftop)

What it does

export2graphlan is a conversion software tool to produce both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format

In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.

For more information, check the user manual.