q2-ps-plot

Qiime2 Plug-in for the creation of visualizations from PepSIRF outputs.

Table of Contents

• Installation

• Tutorial

• Usage

Installation

Qiime2 Installation:

Visit: https://docs.qiime2.org/2021.8/install/ for intallation documentation on Qiime2

PepSIRF Installation:

Visit: https://github.com/LadnerLab/PepSIRF for installation documentation on PepSIRF

q2-ps-plot Installation:

Dependencies:

• qiime2
• PepSIRF
• altair

Directions:

Make sure your Qiime2 conda environment is activated by running the command:

conda activate qiime2-2021.8

You can replace qiime2-2021.8 above with whichever version of QIIME 2 you have currently installed.

Now you are ready to install ps-plot. Run the following commands:

pip install altair
pip install git+https://github.com/LadnerLab/q2-ps-plot.git

Run qiime info to check for a successful installation. If installation was successful, you should see ps-plot: version in the list of installed plugins.

Tutorial

File inputs for tutorial located in q2-ps-plot/example

Running zenrich

Download the following files:

• IM0032-pA_PV1_subset_CS.qza
• IM0032-pA_PV1_subset_Z-HDI95.qza
• pairs_source.tsv

Run the following command:

qiime ps-plot zenrich --i-data IM0032-pA_PV1_subset_CS.qza \
--i-zscores IM0032-pA_PV1_subset_Z-HDI95.qza \
--m-source-file pairs_source.tsv \
--m-source-column Source \
--p-negative-controls SB_pA_A SB_pA_B SB_pA_D \
--o-visualization testing_zenrich

If you cannot run PepSIRF by simply calling 'pepsirf' in the command line, you need to add --p-pepsirf-binary to the above command, followed by how you can call PepSIRF on your system

Once ps-plot has finished running you should see: Saved Visualization to: testing_zenrich.qzv

You can view this visualization by dropping the testing_zenrich.qzv file into https://view.qiime2.org/.

Running zenrich-tsv

Download the following files:

• IM0032-pA_PV1_subset_CS.tsv
• IM0032-pA_PV1_subset_Z-HDI95.tsv
• pairs_source.tsv

Run the following command:

qiime ps-plot zenrich-tsv --p-data-filepath IM0032-pA_PV1_subset_CS.tsv \
--p-zscores-filepath IM0032-pA_PV1_subset_Z-HDI95.tsv \
--m-source-file pairs_source.tsv \
--m-source-column Source \
--p-negative-controls SB_pA_A SB_pA_B SB_pA_D \
--o-zenrich-vis testing_zenrich_tsv

If you cannot run PepSIRF by simply calling 'pepsirf' in the command line, you need to add --p-pepsirf-binary to the above command, followed by how you can call PepSIRF on your system

Once ps-plot has finished running you should see: Saved Visualization to: testing_zenrich_tsv.qzv

You can view this visualization by dropping the testing_zenrich_tsv.qzv file into https://view.qiime2.org/.

Usage

zenrich Arguments

Optional/Required	Argument(s)	Description	Example	Default
Required	--i-data	Featuretable[Normed] - FeatureTable containing normalized read counts of samples and peptides. First column header must be 'Sequence Name' as produced by pepsirf.	--i-data some_file.qza	N/A
Required	--i-zscores	Featuretable[Zscore] - FeatureTable containing z scores of the normalized read counts. Fist column header must be 'Sequence Name' as produced by pepsirf.	--i-zscores some_file.qza	N/A
Optional	--i-negative-data	Featuretable[Normed] - FeatureTable containing normalized read counts of controls and peptides. First column header must be 'Sequence Name' as produced by pepsirf.	-i-negative-data some_file.qza	None
Required	--m-source-file	Metadata file containing all sample names and their source groups. Used to create pairs tsv to run pepsirf enrich module.	--m-source-file some_file.tsv	N/A
Required	--m-source-column	Name of column to collect source info from.	--m-source-column Source	N/A
Optional	--m-peptide-metadata-file	Filename of file that contains peptide metadata related to data to be plotted.	--m-peptide-metadata-file some_file.tsv	None
Required	--p-negative-controls	Sample names of the negative controls to be used.	--p-negative-controls sample1 sample2 sample3	N/A
Optional	--p-tooltip	List of title names found in the peptide metadata file to be added to the hover tooltip (Parameter is case sensitive). 'Peptide' and 'Zscores' will always be added to the list of titles, if peptide metadata is not provided just 'Peptide' and 'Zscores' will be shown.	--p-tooltip Species SpeciesID	['Species', 'SpeciesID'] or None
Optional	--p-step-z-thresh	Integar to increment z-score thresholds.	--p-step-z-thresh 1	5
Optional	--p-upper-z-thresh	Upper limit of z-score thresholds (non-inclusive).	--p-upper-z-thresh 10	30
Optional	--p-lower-z-thresh	Lower limit of z-score thresholds (inclusive).	--p-lower-z-thresh 5	5
Optional	--p-exact-z-thresh	List of exact z score thresholds either individual or combined. List MUST BE in descending order.	--p-exact-z-thresh 25 10 3 or --p-exact-z-thresh 6,25 4,10 1,3	None
Optional	--p-pepsirf-binary	The binary to call pepsirf on your system. Used to call pepsirf enrich module.	--p-pepsirf-binary pepsirf_executable	'pepsirf'
Required	--o-visualization	Visualization output name	--o-visualization file_name.qzv	N/A
Optional	--output-dir	Output unspecified results to a directory	--output-dir directory_name	Current Working Directory

zenrich_tsv Arguments

Optional/Required	Argument(s)	Description	Example	Default
Required	--p-data-filepath	Filepath of .tsv file containing normalized read counts of samples and peptides. First column header must be 'Sequence Name' as produced by pepsirf.	--p-data-filepath some_file.tsv	N/A
Required	--p-zscores-filepath	Filepath of .tsv file containing z scores of the normalized read counts. Fist column header must be 'Sequence Name' as produced by pepsirf.	--p-zscores-filepath some_file.tsv	N/A
Optional	--p-negative-data-filepath	Filepath of .tsv file containing normalized read counts of controls and peptides. First column header must be 'Sequence Name' as produced by pepsirf.	-p-negative-data-filepath some_file.tsv	None
Required	--m-source-file	Metadata file containing all sample names and their source groups. Used to create pairs tsv to run pepsirf enrich module.	--m-source-file some_file.tsv	N/A
Required	--m-source-column	Name of column to collect source info from.	--m-source-column Source	N/A
Optional	--m-peptide-metadata-file	Filename of file that contains peptide metadata related to data to be plotted.	--m-peptide-metadata-file some_file.tsv	None
Required	--p-negative-controls	Sample names of the negative controls to be used.	--p-negative-controls sample1 sample2 sample3	N/A
Optional	--p-tooltip	List of title names found in the peptide metadata file to be added to the hover tooltip (Parameter is case sensitive). 'Peptide' and 'Zscores' will always be added to the list of titles, if peptide metadata is not provided just 'Peptide' and 'Zscores' will be shown.	--p-tooltip Species SpeciesID	['Species', 'SpeciesID'] or None
Optional	--p-step-z-thresh	Integar to increment z-score thresholds.	--p-step-z-thresh 1	5
Optional	--p-upper-z-thresh	Upper limit of z-score thresholds (non-inclusive).	--p-upper-z-thresh 10	30
Optional	--p-lower-z-thresh	Lower limit of z-score thresholds (inclusive).	--p-lower-z-thresh 5	5
Optional	--p-exact-z-thresh	List of exact z score thresholds either individual or combined. List MUST BE in descending order.	--p-exact-z-thresh 25 10 3 or --p-exact-z-thresh 6,25 4,10 1,3	None
Optional	--p-pepsirf-binary	The binary to call pepsirf on your system. Used to call pepsirf enrich module.	--p-pepsirf-binary pepsirf_executable	'pepsirf'
Required	--o-zenrich-vis	Visualization output name	--o-zenrich-vis file_name.qzv	N/A
Optional	--output-dir	Output unspecified results to a directory	--output-dir directory_name	Current Working Directory

More visualizers coming soon...