CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data
Fig 2
CNAViz provides the user with a variety of options, modes, and plots to help the user create an effective segmentation.
(a) Buttons containing import/export options as well as a demo dataset, and allowing the user to import driver genes or use the existing Cancer Genome Census (COSMIC) driver genes. Also includes a drop-down menu for chromosome, the color of the selected bins (default is black), and point size of each bin. (b) Checkboxes controlling the 2D scatter and 1D linear plots. (c) Buttons which lead to pop-ups with analytics, automatic functions, and cluster assignment history. (d) A table summarizing all clusters assigned so far and the percentage of bins represented in each cluster. Also provides the user with the option to change the color for any cluster ID. (e) The toolbar at the top of the screen. The toolbar describing the different modes (Zoom, Pan, Select, Deselect), and their respective hotkeys, will float at the top center of the screen, and the help button is in the top right. (f) Scatter plot with RDR on the y-axis and allelic imbalance on the x-axis. When hovering over a point in the scatter plot, a tooltip appears with information about the corresponding bin including the genomic position, bin size, RDR, allelic imbalance, and cluster ID. In addition, the hovered bin’s position on the linear plots is indicated with a black bar. (g) RDR and allelic imbalance linear plots with genomic position on the x-axis. (h) When points are selected, the color of the bins on all plots changes to a dark blue color. The cluster composition of the selected points is displayed under the plots with a table, where the row color matches the cluster color in the plots. (i) A second sample, where the selected bins are synced across the two samples and across the 2D scatter and 1D linear plots. (j) Driver genes are displayed as red dots along the x-axis of the linear plots. When a driver gene is clicked, it is locked in place and represented as an orange bar with the driver gene symbol above it. Hovering over one of the red dots allows the user to preview the driver gene (displayed as a green vertical bar).