export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. The two output file of export2graphlan should then be used to run graphlan_annotate.py, in order to attach to the tree the derived annotations, and finally, by executing graphlan.py the user can get the output image.
export2graphlan requires the following additional library:
- pandas ver. 0.13.1 (pandas)
- BIOM ver. 2.0.1 (biom-format, only if you have input files in BIOM format)
- SciPy (scipy, required by hclust2)
export2graphlan is available in GitHub here: export2graphlan repository and can be obtained using:
$ conda install export2graphlan
$ pip install export2graphlan
- Repository
$ git clone git@github.com:SegataLab/export2graphlan.git
This will download the export2graphlan repository locally in the export2graphlan subfolder. You then have to put this subfolder into the system path, so that you can use export2graphlan from anywhere in your system:
$ export PATH=`pwd`/export2graphlan/:$PATH
Adding the above line into the bash configuration file will make the path addition permanent. For Windows or MacOS systems a similar procedure should be followed.
usage: export2graphlan.py [-h] [-i LEFSE_INPUT] [-o LEFSE_OUTPUT] -t TREE -a
ANNOTATION [--annotations ANNOTATIONS]
[--external_annotations EXTERNAL_ANNOTATIONS]
[--background_levels BACKGROUND_LEVELS]
[--background_clades BACKGROUND_CLADES]
[--background_colors BACKGROUND_COLORS]
[--title TITLE] [--title_font_size TITLE_FONT_SIZE]
[--def_clade_size DEF_CLADE_SIZE]
[--min_clade_size MIN_CLADE_SIZE]
[--max_clade_size MAX_CLADE_SIZE]
[--def_font_size DEF_FONT_SIZE]
[--min_font_size MIN_FONT_SIZE]
[--max_font_size MAX_FONT_SIZE]
[--annotation_legend_font_size ANNOTATION_LEGEND_FONT_SIZE]
[--abundance_threshold ABUNDANCE_THRESHOLD]
[--most_abundant MOST_ABUNDANT]
[--least_biomarkers LEAST_BIOMARKERS]
[--discard_otus] [--internal_levels]
[--biomarkers2colors BIOMARKERS2COLORS] [--sep SEP]
[--out_table OUT_TABLE] [--fname_row FNAME_ROW]
[--sname_row SNAME_ROW]
[--metadata_rows METADATA_ROWS]
[--skip_rows SKIP_ROWS] [--sperc SPERC]
[--fperc FPERC] [--stop STOP] [--ftop FTOP]
[--def_na DEF_NA]
export2graphlan.py (ver. 0.2.1 of 27 October 2018). Convert MetaPhlAn, LEfSe,
and/or HUMAnN output to GraPhlAn input format. Authors: Francesco Asnicar
(f.asnicar@unitn.it)
optional arguments:
-h, --help show this help message and exit
--annotations ANNOTATIONS
List which levels should be annotated in the tree. Use
a comma separate values form, e.g.,
--annotation_levels 1,2,3. Default is None
--external_annotations EXTERNAL_ANNOTATIONS
List which levels should use the external legend for
the annotation. Use a comma separate values form,
e.g., --annotation_levels 1,2,3. Default is None
--background_levels BACKGROUND_LEVELS
List which levels should be highlight with a shaded
background. Use a comma separate values form, e.g.,
--background_levels 1,2,3. Default is None
--background_clades BACKGROUND_CLADES
Specify the clades that should be highlight with a
shaded background. Use a comma separate values form
and surround the string with " if there are spaces.
Example: --background_clades "Bacteria.Actinobacteria,
Bacteria.Bacteroidetes.Bacteroidia,
Bacteria.Firmicutes.Clostridia.Clostridiales". Default
is None
--background_colors BACKGROUND_COLORS
Set the color to use for the shaded background. Colors
can be either in RGB or HSV (using a semi-colon to
separate values, surrounded with ()) format. Use a
comma separate values form and surround the string
with " if it contains spaces. Example:
--background_colors "#29cc36, (150; 100; 100), (280;
80; 88)". To use a fixed set of colors associated to a
fixed set of clades, you can specify a mapping file in
a tab-separated format, where the first column is the
clade (using the same format as for the "--
background_clades" param) and the second colum is the
color associated. Default is None
--title TITLE If specified set the title of the GraPhlAn plot.
Surround the string with " if it contains spaces,
e.g., --title "Title example"
--title_font_size TITLE_FONT_SIZE
Set the title font size. Default is 15
--def_clade_size DEF_CLADE_SIZE
Set a default size for clades that are not found as
biomarkers by LEfSe. Default is 10
--min_clade_size MIN_CLADE_SIZE
Set the minimum value of clades that are biomarkers.
Default is 20
--max_clade_size MAX_CLADE_SIZE
Set the maximum value of clades that are biomarkers.
Default is 200
--def_font_size DEF_FONT_SIZE
Set a default font size. Default is 10
--min_font_size MIN_FONT_SIZE
Set the minimum font size to use. Default is 8
--max_font_size MAX_FONT_SIZE
Set the maximum font size. Default is 12
--annotation_legend_font_size ANNOTATION_LEGEND_FONT_SIZE
Set the font size for the annotation legend. Default
is 10
--abundance_threshold ABUNDANCE_THRESHOLD
Set the minimun abundace value for a clade to be
annotated. Default is 20.0
--most_abundant MOST_ABUNDANT
When only lefse_input is provided, you can specify how
many clades highlight. Since the biomarkers are
missing, they will be chosen from the most abundant.
Default is 10
--least_biomarkers LEAST_BIOMARKERS
When only lefse_input is provided, you can specify the
minimum number of biomarkers to extract. The taxonomy
is parsed, and the level is choosen in order to have
at least the specified number of biomarkers. Default
is 3
--discard_otus If specified the OTU ids will be discarde from the
taxonmy. Default is True, i.e. keep OTUs IDs in
taxonomy
--internal_levels If specified sum-up from leaf to root the abundances
values. Default is False, i.e. do not sum-up
abundances on the internal nodes
--biomarkers2colors BIOMARKERS2COLORS
Mapping file that associates biomarkers to a specific
color... I'll define later the specific format of this
file!
input parameters:
You need to provide at least one of the two arguments
-i LEFSE_INPUT, --lefse_input LEFSE_INPUT
LEfSe input data. A file that can be given to LEfSe
for biomarkers analysis. It can be the result of a
MetaPhlAn or HUMAnN analysis
-o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT
LEfSe output result data. The result of LEfSe analysis
performed on the lefse_input file
output parameters:
-t TREE, --tree TREE Output filename where save the input tree for GraPhlAn
-a ANNOTATION, --annotation ANNOTATION
Output filename where save GraPhlAn annotation
Input data matrix parameters:
--sep SEP
--out_table OUT_TABLE
Write processed data matrix to file
--fname_row FNAME_ROW
row number containing the names of the features
[default 0, specify -1 if no names are present in the
matrix
--sname_row SNAME_ROW
column number containing the names of the samples
[default 0, specify -1 if no names are present in the
matrix
--metadata_rows METADATA_ROWS
Row numbers to use as metadata[default None, meaning
no metadata
--skip_rows SKIP_ROWS
Row numbers to skip (0-indexed, comma separated) from
the input file[default None, meaning no rows skipped
--sperc SPERC Percentile of sample value distribution for sample
selection
--fperc FPERC Percentile of feature value distribution for sample
selection
--stop STOP Number of top samples to select (ordering based on
percentile specified by --sperc)
--ftop FTOP Number of top features to select (ordering based on
percentile specified by --fperc)
--def_na DEF_NA Set the default value for missing values [default None
which means no replacement]
Note: the last input parameters (Input data matrix parameters) refer to the DataMatrix class contained in the hclust2 repository.
The examples folder contains the following sub-folders: hmp_aerobiosis, hmp_metahit_metabolic, and hmp_metahit_mp2.
Each example should work just by typing in a terminal window (provided that you are inside one of the example folder) the following command:
#!bash
$ ./PIPELINE.sh
If everything goes well you should find in the same folder of the example six new files: annot.txt, outimg.png, outimg_annot.png, outimg_legend.png, outtree.txt, and tree.txt. Where:
annot.txt: contains the annotation that will be used by GraPhlAn, produced by the export2graphlan.py scriptoutimg.png: is the circular tree produced by GraPhlAnoutimg_annot.png: contains the annotation legend of the circular treeoutimg_legend.png: contains the legends of the highlighted biomarkers in the circular treeouttree.txt: is the annotated tree produced by graphlan_annotate.pytree.txt: is the tree produced by the export2graphlan.py script
If you should find problems in using export2graphlan please report them in The bioBakery help forum.