Man pages for AstroPathJHU/mIFTO
mIFTO: Multiplex Immunoflourescence Titration Optimization
| BoxPlot.Calculations | Used by analysis funtions to do the calulations for the... |
| CellbyCell.ByImage | Used by RUN.ByImage to do Cell by Cell Analysis on individual... |
| CellbyCell.BySlide | Used by RUN.BySlide to do Cell by Cell Analysis on images for... |
| check.vars | Check that the input variables are accurate and get a working... |
| create.dir | Create the output directories for either Results.pixels or... |
| create.histo | Used by analysis funtions to generate histogram graphs |
| create.my.theme | Create a common theme for graphs that is relatable to... |
| decile.define.image.positivity | Used by analysis functions to calculate to define image... |
| define.image.positivity | Used by analysis functions to calculate to define image... |
| doupdate.pgbar | Update the progress bar in mIFTO; Created By: Benjamin Green;... |
| FOP | Main function to find the positivity for either tissue, cell... |
| fraction.pos | Used by analysis functions to calculate fraction of... |
| generate.pxp.image.data | Used to create the pixel-by-pixel graph data and return a... |
| Histogram.Calculations | Used by analysis funtions to do the calculations for the... |
| IC.Plots.Calculations | Usedby analysis functions for violin plot calculations |
| ihc.generate.pxp.image.data | Used to create the pixel-by-pixel graph data and return a... |
| ihc.parallel.invoke.gpxp | Used to loop through each image, call the gen func in... |
| map.and.plot.decile.graphs | Used by PxP script to write out the decile type graphs |
| map.and.plot.threshold.graphs | Used by PxP script to write out the threshold type graphs |
| map.and.write.histograms | Used by PxP script to plot out the histograms |
| map.boxplots.plots | Used by PxP script to plot out the boxplots |
| map.ihc.comp.plots | Used by PxP script to write out the fraction of positivity... |
| map.snratio.plots | Used by PxP script to plot out the snratio plots |
| map.ttest.plots | Used by PxP script to plot out the ttests |
| m.grid.arrange | Used to create the figures Created By: Benjamin Green Last... |
| mIFTOapp | Main app to start analysis on a by image basis. Creates the... |
| m.validation | validate that all variables have been populated before moving... |
| parallel.invoke.gpxp | Used to loop through each image, call the gen func in... |
| PixelbyPixel | Used by RUN to do Pixel by Pixel Analysis on individual... |
| populate.tables | Used to loop through each image, call the generate func and... |
| preallocate.tables | Preallocate the tables for the results values; Created By:... |
| server.side | Used by mIFTO to run the main App Created By: Benjamin Green;... |
| SN.Ratio.Calculations | Used by analysis funtions to calculate the signal to noise... |
| sn.ratio.theme | Used by PxP script to create the sn_ratio_theme |
| thresholding.means | Used by analysis functions to calculate the mean signal to... |
| thresholding.medians | Used by analysis functions to calculate the median signal to... |
| thresholding.Noise | Used by analysis funstions to return all noise values above... |
| thresholding.Signal | Used by analysis funstions to return all signal values above... |
| tiff.list | Used by analysis functions to read in 8-layer and 10-layer... |
| ui.formats | Used by mIFTO to run the main App Created By: Benjamin Green;... |
| ui.map | Used by mIFTO to create the UI map Created By: Benjamin... |
| Welch.t.test | Used by analysis functions to perform Welch T-Test on input... |
| welch.t.test.calculations | Used by analysis functions to do the T-Test calculations |
| write.fracs | Used by PxP script to write out the fraction of positivity... |
| write.hist.data | write out the by image histogram data sets Created By:... |
