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fix broken links
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karishma-gangwani committed Oct 29, 2024
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12 changes: 6 additions & 6 deletions docs/Data_Portal/Users_Guide/oncomatrix.md
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Expand Up @@ -55,31 +55,31 @@ The Disco Plot is a circular plot that shows all the mutations and CNVs for a gi

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.

[![Dragging and zooming on case columns](./images/oncomatrix_zoom.png)](./images/oncomatrix_zoom.png 'Click to see the full image.')
[![Dragging and zooming on case columns](./images/oncomatrix/oncomatrix_zoom.png)](./images/oncomatrix/oncomatrix_zoom.png 'Click to see the full image.')

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.

[![Zoom using input control and slider](./images/oncomatrix_zoom2.png)](./images/oncomatrix_zoom2.png 'Click to see the full image.')
[![Zoom using input control and slider](./images/oncomatrix/oncomatrix_zoom2.png)](./images/oncomatrix/oncomatrix_zoom2.png 'Click to see the full image.')

#### Genes

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.

[![Hover over gene](./images/oncomatrix_gene_hover.png)](./images/oncomatrix_gene_hover.png 'Click to see the full image.')
[![Hover over gene](./images/oncomatrix/oncomatrix_gene_hover.png)](./images/oncomatrix/oncomatrix_gene_hover.png 'Click to see the full image.')

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.

[![Click on a gene](./images/oncomatrix_gene_click.png)](./images/oncomatrix_gene_click.png 'Click to see the full image.')
[![Click on a gene](./images/oncomatrix/oncomatrix_gene_click.png)](./images/oncomatrix/oncomatrix_gene_click.png 'Click to see the full image.')

#### Variables

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.

[![Hover over a variable cell](./images/oncomatrix_variable_cell.png)](./images/oncomatrix_variable_cell.png "Click to see the full image.")
[![Hover over a variable cell](./images/oncomatrix/oncomatrix_variable_cell.png)](./images/oncomatrix/oncomatrix_variable_cell.png "Click to see the full image.")

Clicking on a variable allows users to rename it, edit it by excluding categories, replace it with a different variable, or remove it entirely.

[![Click on a variable](./images/oncomatrix_variable_click.png)](./images/oncomatrix_variable_click.png "Click to see the full image.")
[![Click on a variable](./images/oncomatrix/oncomatrix_variable_click.png)](./images/oncomatrix/oncomatrix_variable_click.png "Click to see the full image.")

#### Drag and drop genes and variables

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