PlotsOfDifferences – a web app for the quantitative comparison of unpaired data

Abstract

The quantitative comparison of data acquired under different conditions is an important aspect of experimental science. The most widely used statistic for quantitative comparisons is the pvalue. However, p-values suffer from several shortcomings. The most prominent shortcoming that is relevant for quantitative comparisons is that p-values fail to convey the magnitude of differences. The differences between conditions are best quantified by the determination of effect size. To democratize the calculation of effect size, we have developed a web-based tool. The tool uses bootstrapping to resample mean or median values for each of the conditions and these values are used to calculate the effect size and their compatibility interval. The web tool generates a graphical output, showing the bootstrap distribution of the difference next to the actual data for optimal interpretation. A tabular output with statistics and effect sizes is also generated and the table can be supplemented with p-values that are calculated with a randomization test. The app that we report here is dubbed PlotsOfDifferences and is available at: https://huygens.science.uva.nl/PlotsOfDifferences

Spatiotemporal analysis of host cell modification during herpes simplex virus 1 replication

“…The area of the compartments was then determined using the 'Analyze Particles' function. Violin plots were generated by use of the web app PlotsOfDifferences [41].…”

KMT5C displays robust retention and liquid-like behavior in phase separated heterochromatin

“…Graphical representation of the data was prepared using the PlotsOfDifferences server (https://huygens.science.uva.nl/PlotsOfDifferences/). 31 For partition coefficients, line scans through nuclei of undeconvolved 3D images were recorded using ImageJ. For each cell, the partition coefficient was calculated by subtracting the background level from the maxima of the brightest chromocenter and dividing it by the background corrected fluorescence intensity of the nucleoplasm.…”

“…Statistical significance of sphericity data was evaluated using the embedded stats function within PlotsOfDifferences, which calculates p-values using a randomization test. 31…”

PlotTwist: A web app for plotting and annotating continuous data

“…For static, discrete conditions, dotplots are a good way to graphically depict the data. Several online data visualization tools have been reported that include the option to display the actual data [4][5][6][7][8].…”