# GMine GroupPlots Details

## NestedAnova

Applies a nested anova. Use a nested anova for nested experiment designs " Handbook of Biological Statistics. Example: Measure the impact of a treatment on lab animals in different cages, with treatment as primary group and cage as nested group.

In the nested anova, the "primary group" (3rd column of meta data file) is used as group (e.g. treatment), the secondary group (5th column of meta data file) is used as subgroup (nested group). Standard error is shown as error bars. Only sign. differentially abundant bacterial groups are displayed. Pair-wise comparisons are done by t-test and annotated as *: p<0.05, **: p<0.01, ***: p<0.001.

## RankTestPlot

Sample groups are compared by non-parametric rank test (Wilcoxon rank test for datasets with 2 groups and Kruskal-Wallis test for datasets with more than 2 groups). Significantly differentially abundant bacterial groups are shown as bar chart. Pair-wise comparisons are done by Wilcoxon rank test. Significant differences are annotated by *: p<0.05, **: p<0.01, ***: p<0.001

## AnovaPlot

Significantly different features are shown as barchart (p < 0.05, ANOVA). Standard error is depicted as error bars. Pair-wise comparisons are done by t-test and annotated as *: p<0.05, **: p<0.01, ***: p<0.001

## DistancePlot

Distribution of intra-group and inter-group pair-wise sample distances. Different distance metrics can be used, including Euclidian or Manhattan distance.

## VennDiagram

Venn diagram of features positive (>0) in different sample groups. This plot is only useful for data matrices with values >=0.