Fig. 4

mbImpute preserves distributional characteristics of taxa’s non-zero abundances. a Top: two scatter plots show the relationship between the abundances of Dorea formicigenerans and Ruminococcus torques in Qin et al.’s control samples [19], with or without using mbImpute as a preceding step. The left plot shows two standard major axis (SMA) regression lines and two corresponding Pearson correlations based on the raw data (black: based on all the samples; blue: based on only the samples where both taxa have non-zero abundances). The right plot shows the SMA regression line (blue) and the Pearson correlation using all the samples in the imputed data. Bottom: two scatter plots for the same two taxa in Qin et al.’s T2D samples [19], with lines and legends defined the same as in the top panel. b Four scatter plots show the SMA regression lines and correlations between Eubacterium sirasum and Ruminococcus obeum in Karlsson et al.’s control and T2D samples [18], with lines and legends defined the same as in a. c Each bar shows the Pearson correlation between taxon-taxon correlations in raw data (light gray) or imputed data (dark gray) using all samples and taxon-taxon correlations in raw data using non-zero samples only. The two correlations are calculated for two T2D datasets and four CRC datasets using diseased samples, control samples, and whole data