Publication Plots in R (Self-Study)¶
This page is a self-study reference. It expands the short Day 2 demo on Getting Data Into R into a complete export checklist, every artifact you're likely to want for a publication-quality figure pipeline, plus the steps to set up the workshop's R project and knit visualizations.Rmd into a finished report.
Work through it at your own pace after the workshop. Every export below assumes you're sitting in the working directory you used during Day 2 with core_metrics/, taxonomy_gg2.qza, and the rest of your artifacts in place.
Export α-Diversity Vectors¶
qiime tools export \
--input-path core_metrics/evenness_vector.qza \
--output-path output_for_R
mv output_for_R/alpha-diversity.tsv output_for_R/evenness_vector.tsv
qiime tools export \
--input-path core_metrics/faith_pd_vector.qza \
--output-path output_for_R
mv output_for_R/alpha-diversity.tsv output_for_R/faith_pd_vector.tsv
qiime tools export \
--input-path core_metrics/observed_features_vector.qza \
--output-path output_for_R
mv output_for_R/alpha-diversity.tsv output_for_R/observed_features_vector.tsv
qiime tools export \
--input-path core_metrics/shannon_vector.qza \
--output-path output_for_R
mv output_for_R/alpha-diversity.tsv output_for_R/shannon_vector.tsv
Why the renames?
Every alpha export writes to alpha-diversity.tsv by default, without the immediate mv, each subsequent export overwrites the previous one.
Export β-Diversity Distance Matrices¶
qiime tools export \
--input-path core_metrics/bray_curtis_distance_matrix.qza \
--output-path output_for_R
mv output_for_R/distance-matrix.tsv output_for_R/bray_curtis_distance_matrix.tsv
qiime tools export \
--input-path core_metrics/jaccard_distance_matrix.qza \
--output-path output_for_R
mv output_for_R/distance-matrix.tsv output_for_R/jaccard_distance_matrix.tsv
qiime tools export \
--input-path core_metrics/unweighted_unifrac_distance_matrix.qza \
--output-path output_for_R
mv output_for_R/distance-matrix.tsv output_for_R/unweighted_unifrac_distance_matrix.tsv
qiime tools export \
--input-path core_metrics/weighted_unifrac_distance_matrix.qza \
--output-path output_for_R
mv output_for_R/distance-matrix.tsv output_for_R/weighted_unifrac_distance_matrix.tsv
Export Taxonomy & Feature Table¶
Transpose the feature table and join with sequence and taxonomy data into a single tabulated visualization:
qiime feature-table transpose \
--i-table table_nomitochloro.qza \
--o-transposed-feature-table table_nomitochloro_transposed.qza
qiime metadata tabulate \
--m-input-file table_nomitochloro_transposed.qza \
--m-input-file seqs.qza \
--m-input-file taxonomy_gg2.qza \
--o-visualization tabulated_results.qzv
tabulated_results.qzv opens on view.qiime2.org and exports straight to TSV from the table view.
Export ANCOM-BC2 Results¶
qiime tools export \
--input-path ancombc_sample_type.qza \
--output-path output_for_R/ancombc/sample_type
qiime tools export \
--input-path ancombc_facility.qza \
--output-path output_for_R/ancombc/facility
Export Machine Learning Feature Importances¶
Sample type classifier:
qiime feature-table transpose \
--i-table sample_classifier_results_sample_type/filtered_table_100_features.qza \
--o-transposed-feature-table sample_classifier_results_sample_type/filtered_table_100_features_transposed.qza
qiime metadata tabulate \
--m-input-file sample_classifier_results_sample_type/filtered_table_100_features_transposed.qza \
--m-input-file sample_classifier_results_sample_type/feature_importance.qza \
--o-visualization sample_classifier_results_sample_type/table_100_feature_importances.qzv
Facility classifier:
qiime feature-table transpose \
--i-table sample_classifier_results_facility/filtered_table_100_features.qza \
--o-transposed-feature-table sample_classifier_results_facility/filtered_table_100_features_transposed.qza
qiime metadata tabulate \
--m-input-file sample_classifier_results_facility/filtered_table_100_features_transposed.qza \
--m-input-file sample_classifier_results_facility/feature_importance.qza \
--o-visualization sample_classifier_results_facility/table_100_feature_importances.qzv
Set Up the R Environment¶
Create output directories and copy the workshop's R project files into your working directory:
mkdir R_output_data
mkdir R_figures
cp /pl/active/courses/2025_summer/CSU_2025/q2_workshop_final/R/visualizations.Rmd .
cp /pl/active/courses/2025_summer/CSU_2025/q2_workshop_final/R/R.Rproj .
Open R.Rproj in RStudio and knit visualizations.Rmd to generate the figures. The Rmd reads from output_for_R/ and writes plots to R_figures/.
Final Directory Layout¶
After completing all exports your working directory should look like this: