expression_profiles.html

{% extends 'admin/my_base.html' %}

{% block body %}
{% if form %}
<h1>Add Expression Profile</h1>
<div class="row">
    <div class="col-lg-8 col-md-8 col-sm-6 col-xs-12">
        <form method="POST"  action="{{ url_for('admin_controls.add_expression_profiles') }}"  role="form" enctype="multipart/form-data">
            {{ form.csrf_token }}
            <div class="form-group">
                {{ form.species_id.label }}
                {{ form.species_id(class_="form-control") }}
            </div>
            <div class="form-group">
                {{ form.source.label }}
                {{ form.source(class_="form-control") }}
            </div>
            <div class="form-group">
                <label>The normalized matrix file</label>
                <p>Normalized expression matrix generated using LSTrAP, sequence names should match the names in the database</p>
                <label class="btn btn-default" for="matrix_file" id="matrix-file-button">
                    {{ form.matrix_file(style="display:none;", onchange="")}}
                    <span id="matrix-file-selector-text">Select File</span>
                </label>
            </div>

            <div class="form-group">
                <label>Annotation file</label>
                <p>Text file with two tab-delimited columns with one line header. The first is the sample name, the second a
                condition. Samples with the same condition will be merged.</p>
                <label class="btn btn-default" for="annotation_file" id="annotation-file-button">
                    {{ form.annotation_file(style="display:none;", onchange="")}}
                    <span id="annotation-file-selector-text">Select File</span>
                </label>
            </div>
            <div class="form-group">
                <label>The order and colors for the plot (optional)</label>
                <p>Tab delimited file with the various conditions in order of desired appearance in the plots, here also colors
                can be assigned to each condition in rgba(10,10,10,0.5) format</p>
                <label class="btn btn-default" for="order_colors_file" id="order-colors-file-button">
                    {{ form.order_colors_file(style="display:none;", onchange="")}}
                    <span id="order-colors-file-selector-text">Select File</span>
                </label>
            </div>

            <button type="submit" class="btn btn-primary pull-right">Add Expression Profiles</button>
        </form>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-6 col-xs-12">
        <div class="panel panel-default">
            <div class="panel-heading"><strong>Help</strong></div>
            <div class="panel-body">
                An RPKM or TPM normalized matrix from LSTrAP can be directly used. Furthermore you should include sample
                annotation.
                <br /><br />
                Example for sample annotatation (note the header), two columns are required. The first is the sample ID,
                as it occurs in the matrix (omit the suffix '.htseq'), the second column indicates the condition sampled.
                <br /><br />
                <div class="well">
                    SampleID&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ConditionDescription<br />
                    SRR068956&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068957&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068958&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068959&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068971&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068975&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068976&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068977&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    SRR068987&nbsp;&nbsp;&nbsp;&nbsp;Endosperm<br />
                    ...
                </div>
                Furthermore a file to color code tissues can be provided. Here for each condition a color (that will be
                used in profile plots needs to be specified. Note that the order in this fill will be the order in
                profile plots! Colors need to be in rgba(0-255,0-255,0-255,0-1) format.
                <br /><br />
                <div class="well">
                    Roots (apex), 7 DAG&nbsp;&nbsp;&nbsp;&nbsp;rgba(153, 51, 0, 0.5)<br />
                    Roots (differentation zone), 4 DAP&nbsp;&nbsp;&nbsp;&nbsp;rgba(153, 51, 0, 0.5)<br />
                    ...
                </div>
            </div>
        </div>
    </div>
</div>
{% endif %}

{% endblock %}

{% block tail %}
<script>
    $(function() {
        $("#matrix_file").change(function() {
            $('#matrix-file-selector-text').html($(this).val().replace(/^.*\\/, '') + ' selected');$('#matrix-file-button').toggleClass('btn-default btn-success');
        });
        $("#annotation_file").change(function() {
            $('#annotation-file-selector-text').html($(this).val().replace(/^.*\\/, '') + ' selected');$('#annotation-file-button').toggleClass('btn-default btn-success');
        });
        $("#order_colors_file").change(function() {
            $('#order-colors-file-selector-text').html($(this).val().replace(/^.*\\/, '') + ' selected');$('#order-colors-file-button').toggleClass('btn-default btn-success');
        });
    });
</script>
{{ super() }}
{% endblock%}