Rendering Displays

After performing a gig-map alignment, it can be very helpful to render a visual display of the results. One of the nice features of the gig-map utility is the ability to generate an HTML file which uses the Plotly library to make an interactive map with features for zooming in and expanding specific regions of genetic space. In a previous step, the user should have used the alignment utility of gig-map to generate a set of detailed outputs. In this step, those alignment outputs will be transformed into an HTML file which can be opened and explored by the user.

Generating the Display

Using the render tool, the user may select options for:

• genome_aln: File containing the alignments of genes against genomes, generated by the align_genomes tool as genomes.aln.csv.gz (CSV)
• genome_annot: Genome annotations, keyed on the column 'genome_id' (a template CSV is produced by the align_genomes tool as genome.manifest.csv) (CSV)
• gene_annot: Gene annotations, keyed on the column 'gene_id' (a template CSV is produced by the align_genomes tool as gene.manifest.csv) (CSV)
• genome_distmat: Distance matrix for all genomes, generated by the align_genomes tool as distances.csv.gz
• gene_order: Ordered list of genes, generated by the align_genomes tool as genomes.gene.order.txt.gz (TXT)
• genomeAnnot_label_col: Column in the genome annotation file used to label genomes
• genomeAnnot_color_col: Column in the genome annotation file used for color labeling of genomes (multiple columns may be used with a comma delimiter, e.g. 'species,strain')
• geneAnnot_label_col: Column in the gene annotation file used to label genes
• geneAnnot_color_col: Column in the gene annotation file used for color labeling of genes (multiple columns may be used with a comma delimiter, e.g. 'function,expressed')

Useful References

Other useful references may be:

• Aligning genes to genomes
• Getting started
• Scientific background