misc-data-items

A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-get-sequences-for-gene-clusters anvi-import-misc-data anvi-search-sequence-motifs

Required or used by

anvi-delete-misc-data anvi-export-misc-data

Description

This is the section of your profile-db/pan-db that contains custom additional information about each of the items in the central section of the interactive interface. When you run anvi-interactive, this data will appear as additional concentric circles.

As also defined in this blog post, this type of data will include information about each item (whether that’s a contig, gene, or bin). This data is either numerical or categorical and can be imported into another database from a misc-data-items-txt using anvi-import-misc-data. It is also displayed when you run anvi-show-misc-data and can be exported or deleted with anvi-export-misc-data and anvi-delete-misc-data respectively.

To change the order that the items are displayed in, take a look at anvi-import-items-order.

For example, this information could describe whether or not each bin reached a certain completion threshold, the e-score of the function annotation on each gene, or different categories that the total length of a contig could fall into (1-1.5 kb, 1.5-2 kb, 2-2.5 kb, and so on).

Data groups

Items additional data is organized into data groups. Each group is a named collection of related data keys. For example, when you run anvi-pan-genome, anvi’o automatically creates several groups:

Group	Keys
gene_cluster_stats	num_genomes_gene_cluster_has_hits, num_genes_in_gene_cluster, max_num_paralogs
SCG	SCG
homogeneity	functional_homogeneity_index, geometric_homogeneity_index, combined_homogeneity_index
AAI	AAI_min, AAI_max, AAI_avg

When you import your own data with anvi-import-misc-data without specifying a group (via the -D flag), it goes into the default group.

In the interactive interface, each group gets a checkbox in the Main tab under “Item Data Groups”. You can toggle entire groups on or off to control which layers are displayed. Groups also provide automatic visual separation between related layers.

Note that data key names must be unique across all groups. If you try to import a key that already exists in another group, anvi’o will let you know.

Edit this file to update this information.