Differential analysis & tests / Paired-sample line plot
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Each line joins the two measurements of one subject; red lines go up, blue lines go down. This shows the paired design better than two independent box plots.
Differences are “condition 2 − condition 1” (in the wide layout, the second ticked column minus the first); one-sided tests use the same direction.
The paired t-test assumes roughly normal differences; with skewed differences, outliers or very few pairs use the Wilcoxon signed-rank test. Effect sizes: Cohen’s dz (mean difference / SD of differences) for the t-test and the matched-pairs rank-biserial r for the signed-rank test.
Only subjects with values under both conditions are tested; the page reports how many were left out.
Student (1908) Biometrika 6:1; Wilcoxon (1945) Biometrics Bull 1:80; Pratt (1959) J Am Stat Assoc 54:655; Kerby (2014) Compr Psychol 3:11 (rank-biserial correlation). Statistics and P values match scipy.stats.ttest_rel / wilcoxon (exact null distribution for small samples without ties).
With more than 1,000 pairs the lines become dense; consider plotting a subset.
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