多样性分析

生信喵

一、beta多样性分析

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity core-metrics-phylogenetic \
   
2.   --i-phylogeny rooted-tree.qza \
   
3.   --i-table table.qza \
   
4.   --p-sampling-depth 1103 \
   
5.   --m-metadata-file sample-metadata.tsv \
   
6.   --output-dir core-metrics-results

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二、Alpha多样性分析

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity alpha-group-significance \
   
2.   --i-alpha-diversity core-metrics-results/faith_pd_vector.qza \
   
3.   --m-metadata-file sample-metadata.tsv \
   
4.   --o-visualization core-metrics-results/faith-pd-group-significance.qzv
   
5. 
   
6. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity alpha-group-significance \
   
7.   --i-alpha-diversity core-metrics-results/evenness_vector.qza \
   
8.   --m-metadata-file sample-metadata.tsv \
   
9.   --o-visualization core-metrics-results/evenness-group-significance.qzv

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三、置换多因素方差分析

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity beta-group-significance \
   
2.   --i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
   
3.   --m-metadata-file sample-metadata.tsv \
   
4.   --m-metadata-column body-site \
   
5.   --o-visualization core-metrics-results/unweighted-unifrac-body-site-significance.qzv \
   
6.   --p-pairwise
   
7. 
   
8. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity beta-group-significance \
   
9.   --i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza \
   
10.   --m-metadata-file sample-metadata.tsv \
    
11.   --m-metadata-column subject \
    
12.   --o-visualization core-metrics-results/unweighted-unifrac-subject-group-significance.qzv \
    
13.   --p-pairwise

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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

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime emperor plot \
   
2.   --i-pcoa core-metrics-results/unweighted_unifrac_pcoa_results.qza \
   
3.   --m-metadata-file sample-metadata.tsv \
   
4.   --p-custom-axes days-since-experiment-start \
   
5.   --o-visualization core-metrics-results/unweighted-unifrac-emperor-days-since-experiment-start.qzv
   
6. 
   
7. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime emperor plot \
   
8.   --i-pcoa core-metrics-results/bray_curtis_pcoa_results.qza \
   
9.   --m-metadata-file sample-metadata.tsv \
   
10.   --p-custom-axes days-since-experiment-start \
    
11.   --o-visualization core-metrics-results/bray-curtis-emperor-days-since-experiment-start.qzv

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四、Alpha稀疏曲线

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime diversity alpha-rarefaction \
   
2.   --i-table table.qza \
   
3.   --i-phylogeny rooted-tree.qza \
   
4.   --p-max-depth 4000 \
   
5.   --m-metadata-file sample-metadata.tsv \
   
6.   --o-visualization alpha-rarefaction.qzv

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