多样性分析
一、beta多样性分析docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity core-metrics-phylogenetic \
--i-phylogeny rooted-tree.qza \
--i-table table.qza \
--p-sampling-depth 1103 \
--m-metadata-file sample-metadata.tsv \
--output-dir core-metrics-results
二、Alpha多样性分析
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity alpha-group-significance \
--i-alpha-diversity core-metrics-results/faith_pd_vector.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization core-metrics-results/faith-pd-group-significance.qzv
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity alpha-group-significance \
--i-alpha-diversity core-metrics-results/evenness_vector.qza \
--m-metadata-file sample-metadata.tsv \
--o-visualization core-metrics-results/evenness-group-significance.qzv
三、置换多因素方差分析
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity beta-group-significance \
--i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
--m-metadata-file sample-metadata.tsv \
--m-metadata-column body-site \
--o-visualization core-metrics-results/unweighted-unifrac-body-site-significance.qzv \
--p-pairwise
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity beta-group-significance \
--i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
--m-metadata-file sample-metadata.tsv \
--m-metadata-column subject \
--o-visualization core-metrics-results/unweighted-unifrac-subject-group-significance.qzv \
--p-pairwise排序是在样本元数据的背景下探索微生物群落组成的一种流行方法，对时间分析如下
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime emperor plot \
--i-pcoa core-metrics-results/unweighted_unifrac_pcoa_results.qza \
--m-metadata-file sample-metadata.tsv \
--p-custom-axes days-since-experiment-start \
--o-visualization core-metrics-results/unweighted-unifrac-emperor-days-since-experiment-start.qzv
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime emperor plot \
--i-pcoa core-metrics-results/bray_curtis_pcoa_results.qza \
--m-metadata-file sample-metadata.tsv \
--p-custom-axes days-since-experiment-start \
--o-visualization core-metrics-results/bray-curtis-emperor-days-since-experiment-start.qzv
四、Alpha稀疏曲线
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity alpha-rarefaction \
--i-table table.qza \
--i-phylogeny rooted-tree.qza \
--p-max-depth 4000 \
--m-metadata-file sample-metadata.tsv \
--o-visualization alpha-rarefaction.qzv
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