Study View Customization with Priority Data

Example of study view in public portal: https://www.cbioportal.org/study?id=acc_tcga,lgg_tcga#summary

Priorities

The priority system is represented with a final score. The higher the final (numeric) score, the higher priority assigned.

The default score is 1.

To promote certain chart in study view, please increase priority in the database to a certain number. The higher the score, the higher priority it will be displayed in the study view. If you want to hide chart, please set the priority to 0. For combination chart, as long as one of the clinical attributes has been set to 0, it will be hidden.

Currently, we preassigned priority to few charts, but as long as you assign a priority in the database except than 1, these preassigned priorities will be overwritten.

Chart name(clinical attribute ID)

Frontend default priority

Additional Info

CANCER_TYPE

3000

CANCER_TYPE_DETAILED

2000

Overall Survival Plot

400

This is combination of OS_MONTH and OS_STATUS

Disease Free Survival Plot

300

This is combination of DFS_MONTH and DFS_STATUS

Mutation Count vs. Fraction of Genome Altered Density Plot

200

Mutated Genes Table

90

CNA Genes Table

80

Cancer Studies

70

Number of Samples Per Patient

40

Mutation Count Bar Chart

30

CNA Bar Chart

20

GENDER, SEX

9

AGE

8

Layout

Study view page is fully responsive, it will try to fit more charts in the same height as many as possible base on the browser width.

The layout of a chart is determined mainly based on priority. Higher priority will promote chart closer to the left-top.

In order to improve the layout, we added a layout algorithm layer. The study view page is using grid layout. All charts will be put into 2-dimensional systems. For example, pie chart, by default, takes 1 block and bar chart uses two blocks. All charts will be placed from left to right, top to bottom. In order to prevent misalignment, we promote small charts to fit into the space.