Schema Evaluation and Annotation ================================ This page displays details about a single schema. It also contains a button |back| to return to the :doc:`schemas` page. .. figure:: ../resources/schema_evaluation_overview.png :align: center Figure 1.1: Schema Evaluation and Annotation page. .. |back| image:: ../resources/back_button.png :align: middle Parameters table ---------------- The `chewBBACA `_ parameter table is the same as the one described on the :doc:`schema_overview`. Schema Description ------------------ The Schema Description panel contains the description of the schema provided by the user (in Markdown format) during the schema upload. If the user does not provide a description file, the name of the schema will be used as the schema description. An example file is available at `Chewie-NS' repository `_. For more information on the Markdown specification accepted by Chewie-NS please visit the `Github Flavored Markdown Specification page `_. .. note:: The Schema Description panel is **by default expanded**. It can be collapsed by clicking on the **arrow icon** on the upper-right corner of the panel. .. figure:: ../resources/schema_description.png :align: center Figure 2.1: Schema Description panel. Schema Evaluation ----------------- The Schema Evaluation panel contains 4 plots displaying basic statistics about the schema. The plots are displayed by clicking on the corrresponding buttons. .. note:: The Schema Evaluation panel is **by default expanded**. It can be collapsed by clicking on the **arrow icon** on the upper-right corner of the panel. .. figure:: ../resources/schema_evaluation_expanded.png :align: center Figure 3.1: Expanded Schema Evaluation panel. .. figure:: ../resources/schema_evaluation_collapsed.png :align: center Figure 3.2: Collapsed Schema Evaluation panel. Allele Numbers Analysis ^^^^^^^^^^^^^^^^^^^^^^^ In this plot, **hovering** above the bars will show **how many loci (y-axis)** exibit a **number of different alleles (x-axis)** within the range shown. .. figure:: ../resources/allele_numbers_fig2.png :align: center Figure 4.1: Number of loci (1030) that contain between 50 and 99 alleles. Allele Length Analysis ^^^^^^^^^^^^^^^^^^^^^^ In this plot, **hovering** above the bars will display the **number of loci (y-axis)** having an **allele mode size (x-axis)** within the range shown. .. figure:: ../resources/allele_len.png :align: center Figure 5.1: Number of loci (556) that have an allele mode size in the range 200-249 (bp). Locus Statistics ^^^^^^^^^^^^^^^^ This plot displays the number of alleles, the **median** and the **size range (minimum and maximum)** of the length of each locus. The **y-axis** represents the **number of alleles in the locus** while the **x-axis** represents the **median** and the **size range (minimum and maximum) of the length of the alleles in base pairs**. For example, **Figure 8** shows that Locus 16801 has more than 1500 alleles (y-axis) and that the central tendency measures of allele length are similar are over 5500 base pairs. .. important:: **Clicking** on the plot's data points will take you the :doc:`locus_details` page of that locus! .. figure:: ../resources/locus_statistics.png :align: center Figure 6.1: Locus 16801. Clicking on this point will open a page with the details of locus 16801. Loci Size Variation ^^^^^^^^^^^^^^^^^^^ This plot displays the size variation of all the loci in the schema. The **y-axis** represents the **central tendency measures of the length of the alleles in base pairs** and the **x-axis** represents the each loci. .. important:: **Clicking** on the plot's data points will take you the :doc:`locus_details` page of that locus! .. figure:: ../resources/locus_size_variation_overview.png :align: center Figure 7.1: Loci size variation overview. .. figure:: ../resources/locus_size_variation_zoom.png :align: center Figure 7.2: Locus 15030. Clicking on this point will open a page with the details of locus 15030. Allele Timeline information ^^^^^^^^^^^^^^^^^^^^^^^^^^^ This plot displays the number of alleles added to the schema over time. The **y-axis** represents the **number of alleles added** and the **x-axis** represents the **date** of the allele addition. Annotations ----------- The annotations table contains annotations for each locus of the schema. The columns of the table are the following: - **Uniprot Label**: the Uniprot annotation. - **Uniprot URI**: the URI of the Uniprot annotation. Clicking on the URI will open the page of the relevant Uniprot annotation. - **User locus name**: a recognizable name for the locus provided by the user during the schema upload. - **Custom Annotation**: a custom annotation provided by the user during the schema upload. - **Locus ID**: the ID of the locus. Clicking on the ID will take you to the :doc:`locus_details` page. - **Locus Label**: the Chewie-NS label assigned to the locus. - **Locus Original Name**: the original name of the locus in the original schema or in the genome from which the locus was identified. - **Total Number of Alelles**: the total number of alleles of that locus. - **Alleles Mode (bp)**: the mode of the size of the alleles of that locus in base pairs. - **Size Range (bp)**: the range of sequence lengths of the alleles of that locus in base pairs. .. figure:: ../resources/annotations_table.png :align: center Figure 8.1: Annotations table.