Allow to create a figure similar to the figure 4 of Denise et al 2020 PLoS Biology
Python 3.8
pandas==1.2.0
numpy==1.18.3
matplotlib==3.3.3
biopython==1.76
seaborn==0.11.1
This is a tabular file, the separator is a tabulation (\t). This is a file that contains all the hits that you have for the set of genomes that you use as database.
Need to have a column with an identifier for the genome (chromosome or plasmid) [Replicon_name] and a column that contains the annotation that you want to see the distribution [Your_column_name]
Replicon_name Gene
ACAC001.D.00001.C001 serC
ACAC001.D.00001.C001 pdxP
ACAC001.D.00001.P002 yggS
ACAC001.D.00001.P002 DXS
BAMY001.D.00002.C001 pdxP
BAMY001.D.00002.C001 pdxS
BAMY001.D.00002.C001 pdxT
BAMY001.D.00003.C001 pdxT
BAMY001.D.00003.C001 pdxS
This is a tabular file, the separator is a tabulation (\t). This is the full description of all the species of the database that you used.
The information needed is the same identifier for the genome (chromosome or plasmid) as the Report file [Replicon_name], an identifier for the species to know which replicons belong to the same species [Species_Id] and the full lineage of the species [Lineage]
Replicon_name Species_Id Lineage
ACAC001.D.00001.C001 ACAC001.D.00001 Bacteria;Actinobacteria;Propionibacteriales;Propionibacteriaceae;Acidipropionibacterium
ACAC001.D.00001.P002 ACAC001.D.00001 Bacteria;Actinobacteria;Propionibacteriales;Propionibacteriaceae;Acidipropionibacterium
BAMY001.D.00002.C001 BAMY001.D.00002 Bacteria;Firmicutes;Bacilli;Bacillales;Bacillaceae;Bacillus;Bacillus cereus group
BAMY001.D.00003.C001 BAMY001.D.00003 Bacteria;Firmicutes;Bacilli;Bacillales;Bacillaceae;Bacillus;Bacillus cereus group
A tree of the phyla you want to plot the distribution against in newick format. The phyla need to be present in the lineage of the genomes present in your database.
((Phylum_A,Phylum_B),(Phylum_C,Phylum_D),Phylum_E)
More help with the option -h/--help
usage: phylo_distribution.py [-h] -r <REPORT> -i <INFO_TAB> -c <NAME OF THE COLUMNS OF INTEREST> -t <FILE_TREE>
[-o <FOLDER>] [-order <GENE_NAME/SYSTEM_NAME> [<GENE_NAME/SYSTEM_NAME> ...]]
[-size <SIZE>] [-main_rowspan <INT>] [-tree_colspan <INT>] [-heatmap_colspan <INT>]
[-barplot_rowspan <INT>] [-base_span <INT>] [-height <INT>] [-width <INT>] [-p]
[-color <COLOR>]
Phylegentic Dictribution Figure Creation
optional arguments:
-h, --help show this help message and exit
General input dataset options:
-r <REPORT>, --report <REPORT>
Tabulated File that contain the detection of the genes/systems with the columns
Replicon_name (name of the replicon [for exemple each chromosome of a species is a
different replicon]) and the columns that you want to see the distribution
-i <INFO_TAB>, --infotab <INFO_TAB>
Name of the tabulated file that contain the lineage information for each replicon. Need
to have a columns name Replicon_name (same as in the report), Species_Id (could be the
name of the species, but need to be unique for each genome), Lineage (full lineage of the
genome)
-c <NAME OF THE COLUMNS OF INTEREST>, --columns_distribution <NAME OF THE COLUMNS OF INTEREST>
The name of the column in the report that will be use to do the distribution. The column
contains the annotation for the sequence
-t <FILE_TREE>, --tree_file <FILE_TREE>
The name of tree file of the phyla in newick format
-o <FOLDER>, --output <FOLDER>
Name of the figure where to put the database (default: $PWD/phylo_distribution.pdf)
-order <GENE_NAME/SYSTEM_NAME> [<GENE_NAME/SYSTEM_NAME> ...], --order_columns <GENE_NAME/SYSTEM_NAME> [<GENE_NAME/SYSTEM_NAME> ...]
Ordered list of the genes/systems you want in the heatmap (default: The order of
appearance in the report)
Figure options:
-size <SIZE>, --size_font <SIZE>
Font size in points or as a string (e.g., 'large') (default: 8pt)
-main_rowspan <INT>, --main_rowspan <INT>
Number of row to span the main figure (tree and heatmap) (default: 5)
-tree_colspan <INT>, --tree_colspan <INT>
Number of columns to span the tree (default: 2)
-heatmap_colspan <INT>, --heatmap_colspan <INT>
Number of columns to span the heatmap (default: 8)
-barplot_rowspan <INT>, --barplot_rowspan <INT>
Number of rows to span the barplot under the heatmap (default: 1)
-base_span <INT>, --base_span <INT>
Number of rows/columns to span that are not cited above (defaul: 1)
-height <INT>, --height <INT>
Total height of the figure in point (default: 10)
-width <INT>, --width <INT>
Total width of the figure in point (default: 12)
-color <COLOR>, --color_heatmap <COLOR>
Color of the gradient in the heatmap (default: red)