modules/shinyngs_staticexploratory

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

exploratoryplotboxplotdensityPCA

https://github.com/nf-core/modules/[...]/modules/nf-core/shinyngs/staticexploratory

Description

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

Input

name:type

description

pattern

`meta: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:file`

CSV-format sample sheet with sample metadata

`feature_meta:file`

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

`assay_files:file`

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

Output

name:type

description

pattern

`boxplots_png`

`meta:file`

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

`*/png/boxplot.png:file`

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

`boxplots_html`

`meta:file`

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

`*/html/boxplot.html:file`

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

`densities_png`

`meta:file`

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

`*/png/density.png:file`

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

`densities_html`

`meta:file`

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

`*/html/density.html:file`

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

`pca2d_png`

`meta: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.

`*/png/pca2d.png: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`

`meta: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.

`*/html/pca2d.html: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`

`meta: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.

`*/png/pca3d.png: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`

`meta: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.

`*/html/pca3d.html: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`

`meta: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.

`*/png/mad_correlation.png: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`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*/html/mad_correlation.html:file`

HTML output for MAD correlation plots

*{.html}

`dendro`

`meta:file`

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

`*/png/sample_dendrogram.png: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`

`versions.yml: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

modules/shinyngs_staticexploratory

Description

Input

meta:map

sample:file

feature_meta:file

assay_files:file

Output

boxplots_png

meta:file

*/png/boxplot.png:file

boxplots_html

meta:file

*/html/boxplot.html:file

densities_png

meta:file

*/png/density.png:file

densities_html

meta:file

*/html/density.html:file

pca2d_png

meta:file

*/png/pca2d.png:file

pca2d_html

meta:file

*/html/pca2d.html:file

pca3d_png

meta:file

*/png/pca3d.png:file

pca3d_html

meta:file

*/html/pca3d.html:file

mad_png

meta:file

*/png/mad_correlation.png:file

mad_html

meta:map

*/html/mad_correlation.html:file

dendro

meta:file

*/png/sample_dendrogram.png:file

versions

versions.yml:file

Tools

shinyngs AGPL v3

`meta:map`

`sample:file`

`feature_meta:file`

`assay_files:file`

`boxplots_png`

`meta:file`

`*/png/boxplot.png:file`

`boxplots_html`

`meta:file`

`*/html/boxplot.html:file`

`densities_png`

`meta:file`

`*/png/density.png:file`

`densities_html`

`meta:file`

`*/html/density.html:file`

`pca2d_png`

`meta:file`

`*/png/pca2d.png:file`

`pca2d_html`

`meta:file`

`*/html/pca2d.html:file`

`pca3d_png`

`meta:file`

`*/png/pca3d.png:file`

`pca3d_html`

`meta:file`

`*/html/pca3d.html:file`

`mad_png`

`meta:file`

`*/png/mad_correlation.png:file`

`mad_html`

`meta:map`

`*/html/mad_correlation.html:file`

`dendro`

`meta:file`

`*/png/sample_dendrogram.png:file`

`versions`

`versions.yml:file`

shinyngs
AGPL v3