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docs/Data_Portal/Users_Guide/oncomatrix.md

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@@ -55,31 +55,31 @@ The Disco Plot is a circular plot that shows all the mutations and CNVs for a gi
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To perform an automatic zoom, users can click on and hold a case column then drag the mouse from left to right to form a zoom boundary. From the pop-up window, users can choose to zoom in to the cases, list all highlighted cases, or create a cohort of the selected cases.
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[![Dragging and zooming on case columns](./images/oncomatrix_zoom.png)](./images/oncomatrix_zoom.png 'Click to see the full image.')
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[![Dragging and zooming on case columns](./images/oncomatrix/oncomatrix_zoom.png)](./images/oncomatrix/oncomatrix_zoom.png 'Click to see the full image.')
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The individual case columns are now visible with a demarcated boundary. Above the cases, a slider has been provided for moving from one view to another to accommodate all cases.
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[![Zoom using input control and slider](./images/oncomatrix_zoom2.png)](./images/oncomatrix_zoom2.png 'Click to see the full image.')
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[![Zoom using input control and slider](./images/oncomatrix/oncomatrix_zoom2.png)](./images/oncomatrix/oncomatrix_zoom2.png 'Click to see the full image.')
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#### Genes
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In the panel of genes on the left, users can hover over a gene to view the number of mutated samples, a breakdown of consequence type, and copy number gain and loss counts.
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[![Hover over gene](./images/oncomatrix_gene_hover.png)](./images/oncomatrix_gene_hover.png 'Click to see the full image.')
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[![Hover over gene](./images/oncomatrix/oncomatrix_gene_hover.png)](./images/oncomatrix/oncomatrix_gene_hover.png 'Click to see the full image.')
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Clicking on a gene opens a pop-up window where users can rename it, launch the [ProteinPaint Lollipop plot](proteinpaint_lollipop.md), display the [Gene Summary Page](mutation_frequency.md#gene-and-mutation-summary-pages), and replace or remove the gene. The lollipop plot displays all cases across the GDC affected by SSMs in the selected gene.
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[![Click on a gene](./images/oncomatrix_gene_click.png)](./images/oncomatrix_gene_click.png 'Click to see the full image.')
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[![Click on a gene](./images/oncomatrix/oncomatrix_gene_click.png)](./images/oncomatrix/oncomatrix_gene_click.png 'Click to see the full image.')
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#### Variables
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Any variables added to the matrix appear at the bottom of the plot. Users can hover over a cell in a variable row to display the case submitter_id and their value for the given variable.
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[![Hover over a variable cell](./images/oncomatrix_variable_cell.png)](./images/oncomatrix_variable_cell.png "Click to see the full image.")
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[![Hover over a variable cell](./images/oncomatrix/oncomatrix_variable_cell.png)](./images/oncomatrix/oncomatrix_variable_cell.png "Click to see the full image.")
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Clicking on a variable allows users to rename it, edit it by excluding categories, replace it with a different variable, or remove it entirely.
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[![Click on a variable](./images/oncomatrix_variable_click.png)](./images/oncomatrix_variable_click.png "Click to see the full image.")
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[![Click on a variable](./images/oncomatrix/oncomatrix_variable_click.png)](./images/oncomatrix/oncomatrix_variable_click.png "Click to see the full image.")
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#### Drag and drop genes and variables
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