Nextflow Registry | nf-core/shinyngs/staticexploratory@0.0.0-6c4ed3a

nf-core/shinyngs/staticexploratory @ 0.0.0-6c4ed3a

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

exploratory plot boxplot density PCA

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

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

Add the following snippet to your workflow script to include this module.

include { SHINYNGS_STATICEXPLORATORY } from 'nf-core/shinyngs/staticexploratory'

MIT License

Process

`Name`	`SHINYNGS_STATICEXPLORATORY`

Input 1 channel

#1 tuple

`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 12 channels

#1 dendro tuple

`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.

#2 mad_png tuple

`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.

#3 mad_html tuple

`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}`

#4 pca2d_png tuple

`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.

#5 pca3d_png tuple

`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.

#6 pca2d_html tuple

`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.

#7 pca3d_html tuple

`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.

#8 boxplots_png tuple

`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.

#9 boxplots_html tuple

`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.

#10 densities_png tuple

`meta` file	Meta-keyed tuple containing PNG output for box plots covering input matrices.
`*/png/density.png` file	Meta-keyed tuple containin