Data input requirements:
- Either one or two cohorts.
- One or more numerical nodes or markers from a numerical HDD node.
- Categorical nodes are optional.
After fetching data the Boxplot workflow will draw a box and whiskers plot for every numerical node or gene selected in the previous step. Using the mouse you can zoom in to specific parts of the graphs. If you have created two subsets during cohort selection, you will see boxplots for both groups. Also visible in the workflow are:
- Controls to select data transformations: raw, log2, or log10 transformed.
- A legend that shows the colors for selected groups.
- Controls to change or reset the current view on the data or to download the current image. These controls appear on hover over.
- Also, the plot title shows the result of a calculated ANOVA test for the selected groups.
In each graph in the plot the following is shown:
- Dots with the value for each individual.
- A box that indicates the median and interquartile range, details are shown when you hover over the graph.
- Whiskers that extend up- and downward 1.5 * the IQR.
- A diamond that indicates the mean and confidence level.
When zoomed in, you can reset the view by clicking the auto scaling or reset axes icon in the plot control bar.
The plots control bar has an option to Save and edit plot in cloud. Although there appear to be no issues with this powerful feature, it does upload the generated data to the external plotly service. This makes it potentially available to unauthorized individuals.
- Manual source https://github.com/tranSMART-Foundation/transmartApp-doc/blob/release-16.3/source/smartr.rst
- Hyve manual website http://transmart-app.readthedocs.io/en/latest/
- i2b2 tranSMART Foundation website (available soon)