Calypso GroupPlots Details

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Community profiles of each group are compared and visualized as as boxplot, stripchart or bubbleplot.

Anova Plot

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

Nested Anova

Applies a nested anova. Use a nested anova for nested experiment designs (see Handbook of Biological Statistics for more details). 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) 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.

Rank Test Plot

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

DistancePlot

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

VennDiagram

A bacterial group is marked as present in a sample group if it was identified in at least 40% of the samples within the group. Venn diagrams can only be used for datasets with 2 to 5 groups.


GlobCommunityComp

Microbial profiles are compared using the selected distance measure (Jaccard distance by default). The intra-group and inter-group distances are then compared by Wilcoxon signed-rank test.

Distance Plot

Microbial profiles are compared using the selected distance measure (Jaccard distance by default) and presented as box-plot. The intra-group and inter-group distances are then compared by t-test.