Description

Make exploratory plots for analysis of matrix data, including PCA, Boxplots and density plots

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing information on variables for use in plots, probably experimental information, but at a minimum an id. e.g. [ id:‘treatment’ ]

sample{:bash}

:file

CSV-format sample sheet with sample metadata

feature_meta{:bash}

:file

TSV-format feature (e.g. gene) metadata

assay_files{:bash}

:file

List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).

variable{:bash}

:string

Variable to use for the contrast variable in the plots.

Output

name:type
description
pattern

boxplots_png{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/png/boxplot.png{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

boxplots_html{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/html/boxplot.html{:bash}

:file

Meta-keyed tuple containing HTML output for box plots covering input matrices.

densities_png{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/png/density.png{:bash}

:file

Meta-keyed tuple containing PNG output for density plots covering input matrices.

densities_html{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/html/density.html{:bash}

:file

Meta-keyed tuple containing HTML output for density plots covering input matrices.

pca2d_png{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/png/pca2d.png{:bash}

:file

Meta-keyed tuple containing a PNG output for 2D PCA plots covering specified input matrix (by default the last one in the input list.

pca2d_html{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/html/pca2d.html{:bash}

:file

Meta-keyed tuple containing an HTML output for 2D PCA plots covering specified input matrix (by default the last one in the input list.

pca3d_png{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/png/pca3d.png{:bash}

:file

Meta-keyed tuple containing a PNG output for 3D PCA plots covering specified input matrix (by default the last one in the input list.

pca3d_html{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/html/pca3d.html{:bash}

:file

Meta-keyed tuple containing an HTML output for 3D PCA plots covering specified input matrix (by default the last one in the input list.

mad_png{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/png/mad_correlation.png{:bash}

:file

Meta-keyed tuple containing a PNG output for MAD correlation plots covering specified input matrix (by default the last one in the input list.

mad_html{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/html/mad_correlation.html{:bash}

:file

HTML output for MAD correlation plots

*{.html}

dendro{:bash}

meta{:bash}

:file

Meta-keyed tuple containing PNG output for box plots covering input matrices.

*/png/sample_dendrogram.png{:bash}

:file

Meta-keyed tuple containing a PNG, for a sample clustering dendrogramcovering specified input matrix (by default the last one in the input list.

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

shinyngs
AGPL v3

Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion.

github.com/pinin4fjords/shinyngs rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs https://github.com/pinin4fjords/shinyngs
included in
differentialabundance
maintainer
Github user pinin4fjords
get in touch
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