Qiime2を使った微生物叢の解析（その４）

α、ß多様性解析結果の可視化

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime diversity alpha-group-significance --i-alpha-diversity core-metrics-7118-results/faith_pd_vector.qza --m-metadata-file 20180220_Kazusa-metadata.tsv --o-visualization core-metrics-7118-results/faith-pd-group-significance.qzv

Saved Visualization to: core-metrics-7118-results/faith-pd-group-significance.qzv

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime diversity alpha-group-significance --i-alpha-diversity core-metrics-7118-results/evenness_vector.qza --m-metadata-file 20180220_Kazusa-metadata.tsv --o-visualization core-metrics-7118-results/evenness-group-significance.qzv

Saved Visualization to: core-metrics-7118-results/evenness-group-significance.qzv

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime diversity beta-group-significance --i-distance-matrix core-metrics-7118-results/unweighted_unifrac_distance_matrix.qza --m-metadata-file 20180220_Kazusa-metadata.tsv --m-metadata-column SoilSource --o-visualization core-metrics-7118-results/unweighted-unifrac-soil-source-significance.qzv --p-pairwise

Saved Visualization to: core-metrics-7118-results/unweighted-unifrac-soil-source-significance.qzv

• qiime2-2018.2以降では、以前使われていた --m-metadata-categories のオプションが --m-metadata-column に変更されています。

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime emperor plot --i-pcoa core-metrics-7118-results/unweighted_unifrac_pcoa_results.qza --m-metadata-file 20180220_Kazusa-metadata.tsv --o-visualization core-metrics-7118-results/unweighted-unifrac-emperor.qzv

Saved Visualization to: core-metrics-7118-results/unweighted-unifrac-emperor.qzv

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime emperor plot --i-pcoa core-metrics-7118-results/bray_curtis_pcoa_results.qza --m-metadata-file 20180220_Kazusa-metadata.tsv --o-visualization core-metrics-7118-results/bray-curtis-emperor.qzv

Saved Visualization to: core-metrics-7118-results/bray-curtis-emperor.qzv

Alpha Rarefaction Plotting

(qiime2-2018.2) nedonoiMac:20180112 shigeru$ qiime diversity alpha-rarefaction --i-table table-20180220_Kazusa.qza --i-phylogeny rooted-tree.qza --p-max-depth 64630 --m-metadata-file 20180220_Kazusa-metadata.tsv --o-visualization alpha-rarefaction-Kazusa.qzv

Saved Visualization to: alpha-rarefaction-Kazusa.qzv

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