The PR represents that incorporation of the mechanisms to support the generation of non-intreactive plots via R, Renjin, keeping plot-based analytical insight in the VTEA cytometry workflow. Thus far this has extended to ggplot2 and gplot support for Violin and Heatmap support specifically. To support this functionality VTEA, via the PlotProcessor (extensible via a @SciJava mechanism) and PlotFrame gui, the user can 1) setup SQL queries through swing for the h2 database @h2database with simple and complex feature searches to support visualization (in conjunction with clustering and dimensionality reduction with smile, 2) manage generated plots in a dedicated folder. To support plot export VTEA has also been modified to manage generated files for internal operation including .csv for h2 database and .png files for the PlotProcessor functionality. Example heatmap generated with gplots' heatmap.2:
and via ggplot, violin plots:
These processes can be done inline with visualization (2D via ImagePlus and 3D via ClearVolume), gating and sub-gating via the interactive XY plot and ROIs on the ImagePlus, and rapidly prototyped with changes to image processing and object segmentation.
The PR represents that incorporation of the mechanisms to support the generation of non-intreactive plots via R, Renjin, keeping plot-based analytical insight in the VTEA cytometry workflow. Thus far this has extended to ggplot2 and gplot support for Violin and Heatmap support specifically. To support this functionality VTEA, via the PlotProcessor (extensible via a @SciJava mechanism) and PlotFrame gui, the user can 1) setup SQL queries through swing for the h2 database @h2database with simple and complex feature searches to support visualization (in conjunction with clustering and dimensionality reduction with smile, 2) manage generated plots in a dedicated folder. To support plot export VTEA has also been modified to manage generated files for internal operation including .csv for h2 database and .png files for the PlotProcessor functionality. Example heatmap generated with gplots' heatmap.2:
and via ggplot, violin plots:
These processes can be done inline with visualization (2D via ImagePlus and 3D via ClearVolume), gating and sub-gating via the interactive XY plot and ROIs on the ImagePlus, and rapidly prototyped with changes to image processing and object segmentation.