Added example folder with example files (#7)

* Added example folder with example files * Update README * update readme; change input to estimating-biomass * update readme * flake8 fixes * add est_biomass.csv to example folder * add est_biomass_output.csv to example folder * updated estimating_biomass test * flake8 fix * update unit testing * update unit tests * flake8 fixes * typo fix * typo fix * typo fix * typo fix * change unit test file paths * flake8 fix * fix filepath in tests * flake8 fixes * newer version of qiime2 links added
biocore · Jul 26, 2022 · 57e67de · 57e67de
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diff --git a/README.md b/README.md
@@ -14,35 +14,61 @@ pip install -e .
 
 ## Use
 
-Computation assumes that the user has classified their 16S features against SILVA, and that the `FeatureTable[Frequency]` has been collapsed to the genus level. Please see the [`q2-feature-classifier`](https://docs.qiime2.org/2021.11/plugins/available/feature-classifier/classify-sklearn) for detail on how to perform taxonomy
-classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/available/taxa/collapse) plugin for information on collapsing to a taxonomic level. If you need more information on how to process your data, please refer to one of the relevant tutorials that can be found [here](https://docs.qiime2.org/2022.2/tutorials/).
+Computation assumes that the user has classified their 16S features against SILVA, and that the `FeatureTable[Frequency]` has been collapsed to the genus level. Please see the [`q2-feature-classifier`](https://docs.qiime2.org/2022.2/plugins/available/feature-classifier/classify-sklearn/) for detail on how to perform taxonomy classification, and the [`q2-taxa`](https://docs.qiime2.org/2022.2/plugins/available/taxa/collapse/) plugin for information on collapsing to a taxonomic level. If you need more information on how to process your data, please refer to one of the relevant tutorials that can be found [here](https://docs.qiime2.org/2022.2/tutorials/). For these examples, data from the Fish Microbiome Project (FMP): [Fish microbiomes 101: disentangling the rules governing marine fish mucosal microbiomes across 101 species](https://www.biorxiv.org/content/10.1101/2022.03.07.483203v1) paper will be used, and can be found in the `example` folder.
 
 
-## Obtaining a read count threshold
+## Read Count Threshold
 
-Computation of a minimum read count threshold can be performed with the
-`read_count_threshold` plugin action. Test data can be found under the `testdata` folder.
+In order to obtain a read count threshold, computation of a minimum read count threshold can be performed with the
+`read-count-threshold` plugin action. Test data can be found under the `example` folder.
 
 ```
-qiime katharoseq read_count_threshold \
-    --i-table example/example_table_genus.qza  \ # a genus level table
-    --p-threshold 80 \
+qiime katharoseq read-count-threshold \
+    --i-table example/fmp_collapsed_table.qza \
+    --m-positive-control-column-file example/fmp_metadata.tsv \
+    --m-positive-control-column-column control_rct \
+    --m-cell-count-column-file example/fmp_metadata.tsv \
+    --m-cell-count-column-column control_cell_into_extraction \
+    --p-positive-control-value control \
     --p-control classic \
-    --p-positive-control-value katharoseq_control \ # name of controls in metadata
-    --m-positive-control-column-file example/simple_katharoseq_metadata.tsv \ # your metadata
-    --m-positive-control-column-column control_or_sample \ # sample type variable in metadata
-    --m-cell-count-column-file example/simple_katharoseq_metadata.tsv \
-    --m-cell-count-column-column max_cell_count \ # cell count variable in metadata
-    --o-visualization result.qzv
-```
-qiime katharoseq read_count_threshold \
-    --i-table example.qza \ # a_genus_level_table
-    --p-threshold 80 \
-    --p-control classic \
-    --p-positive-control-value name_of_controls_in_metadata \
-    --m-positive-control-column-file your_metadata.tsv \
-    --m-positive-control-column-column sample_type_variable_in_metadata \
-    --m-cell-count-column-file your_metadata.tsv \
-    --m-cell-count-column-column cell_count_variable_in_metadata \
-    --o-visualization result.qzv
-```
+    --p-threshold 90 \
+    --o-visualization result_fmp_example.qzv
+```
+
+## Estimating Biomass
+
+ Estimate the biomass of samples using KatharoSeq controls. After obtaining a read count threshold using the action above, use the same metadata and collapsed table as input. The `--p-pcr-template-vol` and `--p-dna-template-vol` values are numeric values that should come from your experimental procedures.
+
+```
+qiime katharoseq estimating-biomass \
+    --i-table example/fmp_collapsed_table.qza \
+    --m-control-cell-extraction-file example/fmp_metadata.tsv \
+    --m-control-cell-extraction-column control_cell_into_extraction \
+    --p-min-total-reads 1315 \
+    --p-positive-control-value control \
+    --m-positive-control-column-file example/fmp_metadata.tsv \
+    --m-positive-control-column-column control_rct \
+    --p-pcr-template-vol 5 \
+    --p-dna-extract-vol 60 \
+    --m-extraction-mass-g-column extraction_mass_g \
+    --m-extraction-mass-g-file example/fmp_metadata.tsv \
+    --o-estimated-biomass estimated_biomass_fmp_rct
+```
+
+## Biomass Plot
+
+Finally in order to visualize the results from `estimating-biomass`, run `biomass-plot`.
+
+```
+qiime katharoseq biomass-plot \
+    --i-table example/fmp_collapsed_table.qza \
+    --m-control-cell-extraction-file example/fmp_metadata_mod.tsv \
+    --m-control-cell-extraction-column control_cell_into_extraction \
+    --p-min-total-reads 1315 \
+    --p-positive-control-value control \
+    --m-positive-control-column-file example/fmp_metadata_mod.tsv \
+    --m-positive-control-column-column control_rct \
+    --o-visualization biomass_plot_fmp
+```
+
+