Upload a set of files, each containing the similarities between individuals of a population. KinVis processes these data to compute the individual pairwise lineage similarity, and the population similarities. KinVis can read standard relatedness data in .genome (PLINK) and .kinf (EMMAX) formats. Sample files can be downloaded from bottom of this page.
The user can analyze the populations and individuals in two independent tabs.
In the Populations tab, each population can be selected independently using a checkbox list coming with the standard un/select all, and revert selection buttons. The selected populations can be visualized as a MDS scatterplot and a barchart in 2 sub-tabs when pushing on the Visualize button.
The MDS view shows a multidimensional scaling of the population similarities enabling to discover groups of similar populations. This view can be zoomed and paned to ease exploration of cluttered areas, and the populations there can be selected interactively using a lasso. The user can group-and-name the selected populations. The groups can be downloaded as a csv file. The MDS can be applied to the sole group to analyze local relatedness possibly distorted by the global MDS plot. The percentage of total variance explained by the MDS plot indicates its trustworthiness.
The bar chart view shows for each population, the proportion of pairs of individuals related by a specific color-coded lineage score. A slider allows ordering the population per increasing values up to the selected lineage. It enables to spot rapidly which population contains pairs of individuals with anomalously low lineage score.
In the Individuals tab, the user can choose the population to focus on with a drop-down menu, then all individual data of that population can be selected independently in a checkbox list as for the population tab, and displayed in sub-tabs as two different views.
The heatmap view shows the full details of the pairwise individual color-coded lineage scores. Rows and columns of the matrix are ordered to better see clusters of individuals as blocks with same color.
The node-link view displays the relations (links color-coded by lineage value) between individuals (nodes) for which the lineage score is between the two values set by a double-slider. This node-link visualization can be downloaded as a csv file for further analysis and display with other network visualization softwares.
Groups of selected individuals can be formed as for the populations, to focus the analysis on that group only or on the rest only, using invert selection. All figures can be downloaded as pdf files for optimal quality printing and integration in a report.
All the processed data and groups can be saved locally for later use by saving the workspace. The saved workspace can be uploaded by selecting the workspace file type.
To enforce a fair usage policy, the live server is restricted to process at most 10 files (max size of each file: 2MB). For bigger datasets, you can download kinvis and use its local installation.
This server is run and maintained by Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar.