kevinrue/isee repository overview

⁠General

:white_check_mark: Multiple interactive plot types with selectable points.

:white_check_mark: Interactive tables with selectable rows.

:white_check_mark: Coloring of samples and features by metadata or expression data.

:white_check_mark: Zooming to a plot subregion.

:white_check_mark: Transmission of point selections between panels to highlight, color, or restrict data points in the receiving panel(s).

:white_check_mark: Lasso point selection to define complex shapes.

⁠Sample-level visualization

The iSEE user interface currently contains the following components where each data point represents a single biological sample:

:white_check_mark: Reduced dimension plot: Scatter plot of reduced dimensionality data.

:white_check_mark: Column data plot: Adaptive plot of any one or two sample metadata. A scatter, violin, or square design is dynamically applied according to the continuous or discrete nature of the metadata.

:white_check_mark: Feature assay plot: Adaptive plot of expression data across samples for any two features or one feature against one sample metadata.

:white_check_mark: Column statistics table: Table of sample metadata.

⁠Feature-level visualization

The iSEE user interface currently contains the following components where each data point represents a genomic feature:

:white_check_mark: Row data plot: Adaptive plot of any two feature metadata. A scatter, violin, or square design is dynamically applied according to the continuous or discrete nature of the metadata.

:white_check_mark: Sample assay plot: Adaptive plot of expression data across features for any two samples or one sample against one feature metadata.

:white_check_mark: Row statistics table: Table of feature metadata.

⁠Integrated visualization

The iSEE user interface contains the following components that integrate sample and feature information:

:white_check_mark: Heat map plot: Visualize multiple features across multiple samples annotated with sample metadata.

⁠Custom panels

The iSEE user interface allows users to programmatically define their own plotting and table panels.

:white_check_mark: Custom data plot: Plotting panel that can be assigned any user-defined function returning a ggplot object.

:white_check_mark: Custom statistics table: Table panel that can be assigned any user-defined function returning a data.frame object.

⁠Miscellaneous

:white_check_mark: The iSEE user interface continually tracks the code corresponding to all visible plotting panels. This code is rendered in a shinyAce⁠ text editor and can be copy-pasted into R scripts for customization and further use.

:white_check_mark: Speech recognition can be enabled to control the user interface using voice commands.