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No effect from "--pairwise-comparisons" option in "exportPlots" #970

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github-wow opened this issue Jan 12, 2023 · 0 comments
Open

No effect from "--pairwise-comparisons" option in "exportPlots" #970

github-wow opened this issue Jan 12, 2023 · 0 comments

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@github-wow
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github-wow commented Jan 12, 2023

I did not see expected (?) pair-wise comparison bars and P values above them. Maybe one has to add additional options?

UPD: --pairwise-comparisons group_in_metadata.tsv_file returned error: "Unmatched argument at index 11:'

UPD: --pairwise-comparisons worked with --ref-group group.value_in_metadata.tsv_file but [test name and P value] text block(s) is truncated by image right border.

UPD: --pairwise-comparisons --ref-group group.value_in_metadata.tsv_file --hide-non-significant did not clear nonsignificant [test name and P value] text block(s)

UPD: --pairwise-comparisons --ref-group group.value_in_metadata.tsv_file --hide-non-significant --method ANOVA changed default method to "Anova" (shouldn't it be "ANOVA"?) as an omnibus test on top of the plot but also to "Anova" above the nonreference groups.

UPD: --pairwise-comparisons --ref-group group.value_in_metadata.tsv_file --hide-non-significant --paired --method TTest --method-multiple-groups ANOVA changed the default test above nonreference groups to [T-Test and P value] text blocks.

UPD: --pairwise-comparisons --ref-group group.value_in_metadata.tsv_file --hide-non-significant --paired --method Wilcoxon --method-multiple-groups KruskalWallis results in nonsignificant omnibus tests which do not prevent calculation post hoc tests. Expected horizontal bars appeared but overlay raw data and the [Wilcoxon and P value] text blocks seem to duplicate (and contradict with) the rest P values displayed for the same groups.

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