RD Mapa map to explore rare disease

The default view of RD map
RD Map Default View
The buttons on map toolbar

region-zoom1region zoom used to zoom into a region selected by mouse.

region-zoom2region zoom restore used to restore the view before last region zoom, it supports multiple steps restore.

mouse-zoom1mouse zoom will allow user to zooming and panning by mouse.

mouse-zoom2cancel mouse zoom will disable the mouse zooming and panning events.

browse-mapshow the whole map will restore map view to the default size.

localize-diseaselocalize selected disease the map will show the selected disease in the zoom in center of view.

deselect-diseasedeselect disease it used to deselect the selected disease which will be highlighted when selected by mouse click.

jump-to-anotherjump to gene-based map or jump to phenotype-based map it works only when there is a disease selected and user can jump to another map and localize the same disease. When the selected disease not included in another map there will be a message box.

restore-maprestore map will show the whole map and without clusters information

save-imagesave as image will save current map view as a local image file.

map-settingmap setting will open the following Rare Disease Map Options dialogue box to configure the map by user.

Rare Disease Map Options
Rare Disease Map Options

In this setting, user can configure the mouse click events, whether using the symbol size to reflect prevalence, the default zoom status on different condition, the information will be show on the map. The primary label and secondary label will be shown based on the configured zoom status.

When the user clicks on a common disease point, click event will be triggered, and the disease point will be selected. When the user clicks on a selected disease point, detailed information about the disease will be displayed---Disease Content module.

The default click event is just load the disease name into the Disease Search input box. If you want to learn disease information when click on the disease point, please set it in the click event of Rare Disease Map Options first.

The adjustment range of data zoom is 0-100. The smaller the number set, the smaller the map range when the corresponding event is triggered.

tooltip controls the prompt information displayed when the mouse moves to the disease point. 

label controls the information displayed by the secondary label. The primary label only displays the disease name by default.

RD Map Mappingmap similarity features to RD map

Mapping Mode

After the phenotypes/gene/SNP were selected, here are two mapping mode can be selected using the radio box:

Match is using the exact match approach.

Similarity is using the similarity distance between the description with all diseases.

Only the annotated phenotypes/gene/SNP terms can be used for exact match navigation. Both mapping modes support multiple phenotypes/gene/SNP search.

Do Mapping map the result to the RD map according to user input.

Result Detail trigger dialog box to display specific mapping information.

Match Mapping

Take phenotype match mapping as an example:

Phenotype Match Mapping

As shown in figure above, diseases matched with phenotypes will be highlighted on the RDmap. The left bottom corner will show legends show how many terms were matched, it can also be used to filter the mapping results by click on the legend (the corresponding disease will hide or show on RD map).

User can filter the results by clicking the icon at the bottom left of the map.

Similarity Mapping

Take phenotype similarity mapping as an example:

Phenotype Similarity Mapping1

In the similarity mapping, all diseases on the map will be colored by the similarity score between the searching phenotypes as shown in figure above. The darker of the red color means more similar diseases. The similarity mapping will also show a range slider on the low left corner. User can filter the diseases through adjusting the similarity score range on the slider as shown in figure below. Only several potential diseases will be left after the filtering. User can check the detail information of disease by click on the disease on RD map or click the detail information button of selected disease depending on the setting of RD map.

This function needs to call the background python script for calculation, which usually takes tens of seconds.

Phenotype Similarity Mapping2

User can filter the results by dragging the icons at the bottom left of the map.

Disease Clusterclustering based on phenotype/genotype characteristics

Navigation Workspace --- Disease Cluster

Take phenotype-based RD map as an example:

Disease Cluster

selector select specific cluster.

button-1 display the Rare Disease Cluster Details of selected cluster.

Rare Disease Cluster Details

Take phenotype-based RD map as an example:

Disease Detail all diseases in selected cluster and their brief information.

Cluster Feature Statistic statistics of phenotypic characteristics of all diseases in selected cluster.

High Frequency HPO Top20 Top20 high frequency phenotypes of all diseases in selected cluster.

Disease Contentdisease details

Take phenotype-based RD map as an example:

Disease Content

The detail phenotypes will be shown in a pie chart and list view. Click on the phenotype terms will show the detail definition of the HPO terms. The similar diseases of the target disease also shown as a list on the right (If it is not displayed, please click the Get similar disease button first.) and these diseases can also show on RDmap by click the button Show similarity in chart.

Get similar disease get a list of similar diseases of the selected disease. This function needs to call the background python script for calculation, which usually takes a few seconds.

Show similarity in chart map the similar features between all rare diseases and selected diseases to RD map.

button-1 select the disease to which the button belongs in RD map.

button-2 show the detailed information about disease to which the button belongs.

All icons  are linked to the source of evidence.


All calculation related scripts are available on github.