kraken_res

A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows:

datasets

Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <https://lifemap.cnrs.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.

Aurélie Siberchicot

LifemapR

Data Visualisation on 'Lifemap' Tree

Cassandra Bompard

Damien M. de Vienne

Julien Barnier

kraken_res function

A data frame with 4427 rows and 6 variables:<dl>
<dt>coverage_percent</dt>
<dd>Percentage of fragments covered by the clade rooted at this taxon</dd><dt>coverage_number</dt>
<dd>Number of fragments covered by the clade rooted at this taxon</dd><dt>fragment_number</dt>
<dd>Number of fragments assigned directly to this taxon</dd><dt>rank</dt>
<dd>A rank code, indicating (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. Taxa that are not at any of these 10 ranks have a rank code that is formed by using the rank code of the closest ancestor rank with a number indicating the distance from that rank. E.g., "G2" is a rank code indicating a taxon is between genus and species and the grandparent taxon is at the genus rank.</dd><dt>taxid</dt>
<dd>NCBI taxonomic ID number</dd><dt>name</dt>
<dd>Indented scientific name</dd>
</dl>

Format

Kraken results — kraken_res

A data frame with 4427 rows and 6 variables:<dl>
<dt>coverage_percent</dt>
<dd>Percentage of fragments covered by the clade rooted at this taxon</dd>

<dt>coverage_number</dt>
<dd>Number of fragments covered by the clade rooted at this taxon</dd>

<dt>fragment_number</dt>
<dd>Number of fragments assigned directly to this taxon</dd>

<dt>rank</dt>
<dd>A rank code, indicating (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. Taxa that are not at any of these 10 ranks have a rank code that is formed by using the rank code of the closest ancestor rank with a number indicating the distance from that rank. E.g., "G2" is a rank code indicating a taxon is between genus and species and the grandparent taxon is at the genus rank.</dd>

<dt>taxid</dt>
<dd>NCBI taxonomic ID number</dd>

<dt>name</dt>
<dd>Indented scientific name</dd>


</dl>

kraken_res: Kraken results

Description

Usage

Arguments

Format