Comments (1)
Hi @Lcornet ,
There isn't currently a way to restrict anvi-display-functions
to a specific set of annotations within a given annotation source. However, I can think of one workaround:
- export the KOfam functions from each contigs database using
anvi-export-functions
- filter the (db-specific) functions list to your KOfams of interest
- import the filtered list of KOfams into each contigs database with a unique annotation source name (for example, 'KOfam_filtered'), with
anvi-import-functions
- run
anvi-display-functions
with the new annotation source name describing the filtered KOs
For your second question, I think you could order by sugar source by importing the sugar source information per item in the display, so that this additional data field will then show up in Order By box on the interface. This can be done pretty easily by using anvi-import-misc-data
on your profile database before you re-visualize it using anvi-interactive --manual
. The tricky bit will be to figure out which item name belongs to each KOfam, since functions in this display are described via a hash value, not the KO accession itself. I am guessing that a workflow like this could work:
- generate your initial display with
anvi-display-functions
to get a profile database - export the KO associated with each item, and the item's name (hash value) using
anvi-export-misc-data
(you will need to export the items table) - create a new items misc data file mapping the sugar source to each item based upon its associated KOfam annotation
- import that new data file into the existing profile database (the items additional data table again) using
anvi-import-misc-data
. - visualize the display again using
anvi-interactive --manual
and giving the program the path to your profile database - then you should see the sugar source additional data value as an option for ordering the display.
The documentation for all of the programs mentioned here (and their associated artifacts) can be found on the anvi'o website. Hopefully it is clear enough that you can figure out the parameters you need for each step. If not, let us know.
from anvio.
Related Issues (20)
- [FEATURE REQUEST] Annotate which KOfams were added by our bitscore relaxation heuristic
- [FEATURE REQUEST] A conda package for anvi'o with a minimal installation option HOT 1
- [BUG] `--prodigal-single-mode` breaks metagenomic workflow HOT 5
- [BUG] anvio-cluster-contigs fails with Generate input data
- [BUG] anvi-meta-pan-genome does not allow me to use gene calls not from prodigal HOT 10
- [BUG] Missing USearch in installation instruction and workflow DAG declarations HOT 1
- [BUG] contigs.db has issues when inputing aa_sequence in the external-gene-call file HOT 9
- [BUG] MaxBin2 failing due to one missing coverage HOT 2
- [BUG] anvio installation HOT 15
- [BUG] Pandas dataframe has no attribute 'append' HOT 4
- [BUG] Pandas error in `anvi-get-codon-frequencies` HOT 6
- [BUG] ERROR in running anvi-script-gen_stats_for_single_copy_genes.R HOT 1
- [FEATURE REQUEST] Using external gene clusters for anvi-pan-genome HOT 1
- [FEATURE REQUEST] Case-sensitive search in `anvi-export-locus` HOT 6
- [BUG] The CONTIGS.db file is 0kb and slurm job is still running HOT 2
- Interactive interface, TypeError: Cannot read properties of undefined (reading 'angle') when trying to organize by length HOT 5
- [FEATURE REQUEST] adding contigs database names to deflines of exported genes/proteins fasta HOT 2
- [BUG] cannot import vbgmm in concoct
- [BUG] anvi-pan-genome - diamond BUG
- Running anvio through snakemake, no errors but the job submission stops running HOT 12
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from anvio.