A visualisation tool based on d3.js for probe pairs arising in genome wide association studies.
An online demo is available as a gist and is viewable on Mike Bostock's bl.ocks.org.
- Cheng Soon Ong
- Justin Bedo
- Cristovao Freitas Iglesias Junior
- Stefan Sevelda
Browser: Mozilla Firefox (for development version 27.0.1 was used).
Open view_graph.html with Mozilla Firefox. Click the "Browse..." button and select a json file with the right format(see section file format). There are four different types of plots in the "plots" dropbox:
- Circular ideogram
- Manhattan plot
- Heat-map
- Arc plot
Statistical test:
If you selected the Circular plot a dropbox with the available statistical tests will appear. The p-values of the SNP interactions will be displayed under the statistical test dropbox on an axis. You could select an arbitrary area of values through clicking on the axis and moving the mouse. The selected area is brushed and you can move it with the mouse afterwards.
Probe groups:
In the section Probe group you will see a histogram of the connected edges of the probe groups. If you click on a bar the selected probe group will appear in the circular plot. You can collapse the section probe group through clicking on the "-" in the header.
SNPs histogram:
In the SNPs section you will find a histogram of all SNPs and the degree of connection to other SNPs. If you click on a bar only the direct connections of this SNP will be displayed in the plot. The bar of the selected SNP will be displayed in green and the connected SNPs will be displayed in red. If you click on the text of the SNP a prompt window with common literature sources will open where you can search for additional information of the selected SNP. This literature window will also appear after clicking on a SNP node in the circular plot. You can also collapse the SNPs histogram if you like.
SNPs Pairs list:
The SNPs Pairs section lists all the links of the selected dataset. You can sort the links by the selected statistical test in the "Sort by" dropbox. If you select a specific area of p-value on the axis or select a probe group only these SNP-links will be listed. You can also highlight a link in the SNPs Pairs section through clicking on the desired connection in the plot. If you want to get more information about a specific link you only have to click on the paragraph of the link in the SNPs Pairs section and a ROC plot and a contingency table about this connection will appear above the SNPs section. You can also collapse the section if you like.
Zoom function:
If you select a chromosome in the top of the page,type a specific start base, end base and click on the zoom button you will receive a circular plot with the desired area. All described features in the upper section are also available for the zoomed plot. If you want to go back to the unzoomed plot press the "Reset" button.
Like in the circular ideogram you can choose the statistical test in the left top.
Labeling:
If you push the label button in the right top of the window information to every node will appear in the plot. You can remove the labels through clicking the "remove_label" button.
Zoom function:
You can select an area with the mouse in the plot and after pushing the zoom button in the upper left of the window the selected area will be displayed. The labeling function is also available for the zoomed area. Through clicking the "Reset" button you go back to the unzoomed manhattan plot.
If you select the heat-map in the "Plots" dropbox two dropboxes will appear under the heat-map. You can select the desired statistical test there.
Zoom function:
Is working like the zoom function of the manhattan plot. You have also the SNPs list included with all the features described in the circular plot, excepted that if you click on the degree-bar not only the selected SNPs will appear.
The arc plot has the same features like the circular plot. Additional to that you can select a certain area through brushing with the mouse in the plot as well. For this feature you select a chromosome and push the "zoom" button. Afterwards you can click on the selected chromosome and mark a desired area. After that you click on the "zoom" button and you zoomed in the selected area. To get back at the unzoomed plot you only have to click the "Reset" button.
The visualised data has to be a .json file
This is a description of the json file format used to store the epistatic graph.
{
"type": "object",
"properties": {
"type": "array",
"items": {
"type": [
"nodes": {
"description": "Information about single SNPs",
"type": "objects"
"properties": {
"prbCode": {
"description": "Id for the probe",
"type": "string"
},
"degree": {
"description": "Number of interactions",
"type": "number"
},
"prb": {
"description": "Index of probe",
"type": "number"
},
"rs": {
"description": "The rs number",
"type": "string"
},
"probe_group": {
"description": "Id of the connected subgraph",
"type": "number"
},
"bp_position": {
"description": "position on the chromosome",
"type": "number"
},
"chrom": {
"description": "The chromosome",
"type": "number"
},
"id": {
"description": "Unique id of SNP",
"type": "number"
}
},
"required": ["prbCode", "degree", "prb", "rs",
"probe_group", "bp_position", "chrom", "id"]
}
]
},
"type": "array",
"items": {
"type": [
"links": {
"type": "object",
"properties": {
"source": {
"description": "Id of the source SNP",
"type": "number"
},
"target": {
"description": "Id of the target SNP",
"type": "number"
},
"probe_group": {
"description": "The subgraph of the link",
"type": "number"
},
"<statistical testsname>": {
"description": "Statistical test(there can be
multiple tests)",
"type": "number"
},
"ct_id": {
"description": "Unique id of link",
"type": "number"
}
},
"required"["source", "target", "probe_group",
"<statistical testsname>", "ct_id"]
}
]
},
"type": "array",
"items": {
"type": [
"cont_table": {
"description": "Information about contigency table",
"type": "object",
"properties": {
"unv1": {
"description": "univariate table for source
(could appear multiple times)",
"type": "object",
"properties": {
"controls": {
"description": "control group number",
"type": "number"
},
"cases": {
"description": "case group number",
"type": "number"
}
},
"required": ["controls", "cases"]
},
"unv2": {
"description": "univariate table for
target(could appear multiple times)",
"type": "object",
"properties": {
"controls": {
"description": "control group number",
"type": "number"
},
"cases": {
"description": "case group number",
"type": "number"
}
},
"required": ["controls", "cases"]
},
"biv": {
"description": "bivariate table(could appear
multiple times)",
"type": "object",
"properties": {
"controls": {
"description": "control group number",
"type": "number"
},
"cases": {
"description": "case group number",
"type": "number"
}
},
"required": ["controls", "cases"]
},
"total": {
"description": "total amount of individuals",
"type": "object",
"properties": {
"controls": {
"description": "control group number",
"type": "number"
},
"cases": {
"description": "case group number",
"type": "number"
}
},
"required": ["controls", "cases"]
}
},
"required": ["unv1", "unv2", "biv", "total"]
}
]
},
"type": "array",
"items": {
"type": [
"communities": {
"descirption": "shows the communities ...",
"type": "number",
}
]
},
"required": ["nodes", "links", "cont_table"]
}
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