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).

`variable`
`:string`

Variable to use for the contrast variable in the plots.

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 PNG 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 box 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 PNG output for box 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 PNG output for box plots covering input matrices.

`*/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 PNG output for box plots covering input matrices.

`*/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 PNG output for box plots covering input matrices.

`*/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 PNG output for box plots covering input matrices.

`*/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 PNG output for box plots covering input matrices.

`*/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`
`:file`

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

`*/html/mad_correlation.html`
`:file`

HTML output for MAD correlation plots

*{.html}

`dendro`

`meta`
`:file`

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

`*/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_shinyngs`

`${task.process}`
`:string`

The name of the process

`shinyngs`
`:string`

The name of the tool

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`shinyngs`
`:string`

The name of the tool

`Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))"`
`:eval`

The expression to obtain the version of the tool

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 pinin4fjords.github.io/shinyngs https://github.com/pinin4fjords/shinyngs