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{%extends "phenotypes/add-phenotypes-base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%from "macro-table-pagination.html" import table_pagination%}
{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
{%block title%}Phenotypes{%endblock%}
{%block pagetitle%}Phenotypes{%endblock%}
{%block lvl4_breadcrumbs%}
<li {%if activelink=="add-phenotypes"%}
class="breadcrumb-item active"
{%else%}
class="breadcrumb-item"
{%endif%}>
<a href="{{url_for('species.populations.phenotypes.add_phenotypes',
species_id=species.SpeciesId,
population_id=population.Id,
dataset_id=dataset.Id)}}">Add Phenotypes</a>
</li>
{%endblock%}
{%block frm_add_phenotypes_documentation%}
<p>Select the zip file bundle containing information on the phenotypes you
wish to upload, then click the "Upload Phenotypes" button below to
upload the data.</p>
<p>If you wish to upload the files individually instead,
<a href="{{url_for('species.populations.phenotypes.add_phenotypes',
species_id=species.SpeciesId,
population_id=population.Id,
dataset_id=dataset.Id)}}"
title="">click here</a>.</p>
<p>See the <a href="#section-file-formats">File Formats</a> section below
to get an understanding of what is expected of the bundle files you
upload.</p>
{%endblock%}
{%block frm_add_phenotypes_elements%}
<div class="form-group">
<label for="finput-phenotypes-bundle" class="form-label">
Phenotypes Bundle</label>
<input type="file"
id="finput-phenotypes-bundle"
name="phenotypes-bundle"
accept="application/zip, .zip"
required="required"
class="form-control" />
</div>
{%endblock%}
{%block page_documentation%}
<div class="row">
<h2 class="heading" id="section-file-formats">File Formats</h2>
<p>We accept an extended form of the
<a href="https://kbroman.org/qtl2/assets/vignettes/input_files.html#format-of-the-data-files"
title="R/qtl2 software input file format documentation">
input files' format used with the R/qtl2 software</a> as a single ZIP
file</p>
<p>The files that are used for this feature are:
<ul>
<li>the <em>control</em> file</li>
<li><em>pheno</em> file(s)</li>
<li><em>phenocovar</em> file(s)</li>
<li><em>phenose</em> files(s)</li>
</ul>
</p>
<p>Other files within the bundle will be ignored, for this feature.</p>
<p>The following section will detail the expectations for each of the
different file types within the uploaded ZIP file bundle for phenotypes:</p>
<h3 class="subheading">Control File</h3>
<p>There <strong>MUST be <em>one, and only one</em></strong> file that acts
as the control file. This file can be:
<ul>
<li>a <em>JSON</em> file, or</li>
<li>a <em>YAML</em> file.</li>
</ul>
</p>
<p>The control file is useful for defining things about the bundle such as:</p>
<ul>
<li>The field separator value (default: <code>sep: ','</code>). There can
only ever be one field separator and it <strong>MUST</strong> be the same
one for <strong>ALL</strong> files in the bundle.</li>
<li>The comment character (default: <code>comment.char: '#'</code>). Any
line that starts with this character will be considered a comment line and
be ignored in its entirety.</li>
<li>Code for missing values (default: <code>na.strings: 'NA'</code>). You
can specify more than one code to indicate missing values, e.g.
<code>{…, "na.strings": ["NA", "N/A", "-"], …}</code></li>
</ul>
<h3 class="subheading"><em>pheno</em> File(s)</h3>
<p>These files are the main data files. You must have at least one of these
files in your bundle for it to be valid for this step.</p>
<p>The data is a matrix of <em>individuals × phenotypes</em> by default, as
below:<br />
<code>
id,10001,10002,10003,10004,…<br />
BXD1,61.400002,54.099998,483,49.799999,…<br />
BXD2,49,50.099998,403,45.5,…<br />
BXD5,62.5,53.299999,501,62.900002,…<br />
BXD6,53.099998,55.099998,403,NA,…<br />
⋮<br /></code>
</p>
<p>If the <code>pheno_transposed</code> value is set to <code>True</code>,
then the data will be a <em>phenotypes × individuals</em> matrix as in the
example below:<br />
<code>
id,BXD1,BXD2,BXD5,BXD6,…<br />
10001,61.400002,49,62.5,53.099998,…<br />
10002,54.099998,50.099998,53.299999,55.099998,…<br />
10003,483,403,501,403,…<br />
10004,49.799999,45.5,62.900002,NA,…<br />
⋮
</code>
</p>
<h3 class="subheading"><em>phenocovar</em> File(s)</h3>
<p>At least one phenotypes metadata file with the metadata values such as
descriptions, PubMed Identifier, publication titles (if present), etc.</p>
<p>The data in this/these file(s) is a matrix of
<em>phenotypes × phenotypes-covariates</em>. The first column is always the
phenotype names/identifiers — same as in the R/qtl2 format.</p>
<p><em>phenocovar</em> files <strong>should never be transposed</strong>!</p>
<p>This file <strong>MUST</strong> be present in the bundle, and have data for
the bundle to be considered valid by our system for this step.<br />
In addition to that, the following are the fields that <strong>must be
present</strong>, and
have values, in the file before the file is considered valid:
<ul>
<li><em>description</em>: A description for each phenotype. Useful
for users to know what the phenotype is about.</li>
<li><em>units</em>: The units of measurement for the phenotype,
e.g. milligrams for brain weight, centimetres/millimetres for
tail-length, etc.</li>
</ul></p>
<p>The following <em>optional</em> fields can also be provided:
<ul>
<li><em>pubmedid</em>: A PubMed Identifier for the publication where
the phenotype is published. If this field is not provided, the system will
assume your phenotype is not published.</li>
</ul>
</p>
<p>These files will be marked up in the control file with the
<code>phenocovar</code> key, as in the examples below:
<ol>
<li>JSON: single file<br />
<code>{<br />
⋮,<br />
"phenocovar": "your_covariates_file.csv",<br />
⋮<br />
}
</code>
</li>
<li>JSON: multiple files<br />
<code>{<br />
⋮,<br />
"phenocovar": [<br />
"covariates_file_01.csv",<br />
"covariates_file_01.csv",<br />
⋮<br />
],<br />
⋮<br />
}
</code>
</li>
<li>YAML: single file or<br />
<code>
⋮<br />
phenocovar: your_covariates_file.csv<br />
⋮
</code>
</li>
<li>YAML: multiple files<br />
<code>
⋮<br />
phenocovar:<br />
- covariates_file_01.csv<br />
- covariates_file_02.csv<br />
- covariates_file_03.csv<br />
…<br />
⋮
</code>
</li>
</ol>
</p>
<h3 class="subheading"><em>phenose</em> and <em>phenonum</em> File(s)</h3>
<p>These are extensions to the R/qtl2 standard, i.e. these types ofs file are
not supported by the original R/qtl2 file format</p>
<p>We use these files to upload the standard errors (<em>phenose</em>) when
the data file (<em>pheno</em>) is average data. In that case, the
<em>phenonum</em> file(s) contains the number of individuals that were
involved when computing the averages.</p>
<p>Both types of files are matrices of <em>individuals × phenotypes</em> by
default. Like the related <em>pheno</em> files, if
<code>pheno_transposed: True</code>, then the file will be a matrix of
<em>phenotypes × individuals</em>.</p>
</div>
{%endblock%}
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