Ps-qc Tutorials - CLI Edition (more to come)

Introduction

In this tutorial you’ll use QIIME 2 to perform an analysis of some data.

Typical Runtime: 0 Minutes 15.43 Seconds

Description

This guide is a preview of how you can use some of q2-ps-qc’s individual modules.

Generate a Correlation Matrix

Here we will test q2-ps-qc’s generate-corr-matrix module by running the following command:

import qiime2.plugins.q2_ps_qc.actions as q2_ps_qc_actions

bad_corr_viz, good_corr_viz = q2_ps_qc_actions.generate_corr_matrix(
    data='source/data/IM0032-pA_PV1_subset_CS.tsv',
)

library(reticulate)

q2_ps_qc_actions <- import("qiime2.plugins.q2_ps_qc.actions")

action_results <- q2_ps_qc_actions$generate_corr_matrix(
    data='source/data/IM0032-pA_PV1_subset_CS.tsv',
)
bad_corr_viz <- action_results$bad_output
good_corr_viz <- action_results$good_output

qiime q2-ps-qc generate-corr-matrix \
  --p-data source/data/IM0032-pA_PV1_subset_CS.tsv \
  --o-bad-output bad-corr.qzv \
  --o-good-output good-corr.qzv

bad_corr_vis, good_corr_vis = use.action(
        use.UsageAction(
                plugin_id="q2_ps_qc",
                action_id="generate_corr_matrix"
        ),
        use.UsageInputs(
                data="source/data/IM0032-pA_PV1_subset_CS.tsv"
        ),
        use.UsageOutputNames(
                bad_output="bad_corr",
                good_output="good_corr"
        )
)
Using the qiime2 q2-ps-qc generate-corr-matrix tool:

  1. Set “data” to source/data/IM0032-pA_PV1_subset_CS.tsv

  2. Press the Execute button.

Once completed, for each new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name

“Name” to set (be sure to press Save)

#: qiime2 q2-ps-qc generate-corr-matrix [...] : bad_output.qzv

bad-corr.qzv

#: qiime2 q2-ps-qc generate-corr-matrix [...] : good_output.qzv

good-corr.qzv