You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/Data_Portal/Users_Guide/oncomatrix.md
+6-6Lines changed: 6 additions & 6 deletions
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -55,31 +55,31 @@ The Disco Plot is a circular plot that shows all the mutations and CNVs for a gi
55
55
56
56
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.
57
57
58
-
[](./images/oncomatrix_zoom.png'Click to see the full image.')
58
+
[](./images/oncomatrix/oncomatrix_zoom.png'Click to see the full image.')
59
59
60
60
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.
61
61
62
-
[](./images/oncomatrix_zoom2.png'Click to see the full image.')
62
+
[](./images/oncomatrix/oncomatrix_zoom2.png'Click to see the full image.')
63
63
64
64
#### Genes
65
65
66
66
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.
67
67
68
-
[](./images/oncomatrix_gene_hover.png'Click to see the full image.')
68
+
[](./images/oncomatrix/oncomatrix_gene_hover.png'Click to see the full image.')
69
69
70
70
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.
71
71
72
-
[](./images/oncomatrix_gene_click.png'Click to see the full image.')
72
+
[](./images/oncomatrix/oncomatrix_gene_click.png'Click to see the full image.')
73
73
74
74
#### Variables
75
75
76
76
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.
77
77
78
-
[](./images/oncomatrix_variable_cell.png"Click to see the full image.")
78
+
[](./images/oncomatrix/oncomatrix_variable_cell.png"Click to see the full image.")
79
79
80
80
Clicking on a variable allows users to rename it, edit it by excluding categories, replace it with a different variable, or remove it entirely.
81
81
82
-
[](./images/oncomatrix_variable_click.png"Click to see the full image.")
82
+
[](./images/oncomatrix/oncomatrix_variable_click.png"Click to see the full image.")
0 commit comments