colourededgerxlsx

Outputs an xlsx file with one tab for each contrast in a table, with colours for SEED categories and heatmaps for logFC, logCPM and FDR.

Overview

The main input for the script is a table with top tags from an EdgeR analysis. The table should have all columns from an extracted top tags table, plus a column called "contrasts".

The input file should look like this:

In the current version -- 0.1 -- given one or more SEED annotation tables keyed by feature one can produce a spreadsheet with two tabs for each contrast, one with all features with FDR <= 0.10 and one with all:

Colours -- ugly but relatively distinct -- are currently hardcoded in the script.

Installation

Clone the repository and make sure the src/R/colourededgerxlsx.r is in your path, potentially by symlinking to it. E.g.:

$ cd ~/dev
$ git clone https://github.com/erikrikarddaniel/colourededgerxlsx.git
$ cd ~/bin
$ ln -s ../dev/colourededgerxlsx/src/R/colourededgerxlsx.r .

Usage

There's a --help flag to the script that explains how to call it. Here are a few examples.

Only SEED annotation(s)

A typical call with only a SEED annotation looks like this:

$ colourededgerxlsx.r --verbose \
  --seedtables=genome1.SEED.tsv,genome2.BAL450.SEED.tsv \
  --outxlsx=coloured_edger.xlsx \
  edger_table.tsv.gz

Note in the above that two genomes were involved. Just type a comma-separated list of SEED annotation files.

Secondary annotation

If your SEED annotation isn't complete (typical case) you can add a second set of annotations. These tables must only have two columns: one is the key, and that must be the same as in the EdgeR table and SEED annotations, the other a column with any name.

$ colourededgerxlsx.r --verbose \
  --seedtables=genome1.SEED.tsv,genome2.BAL450.SEED.tsv \
  --annottables=genome1.rast.tsv,genome2.rast.tsv \
  --outxlsx=coloured_edger.xlsx \
  edger_table.tsv.gz

Future plans

• Version 0.3: Parse EC numbers from SEED or other annotation to new column

• Version 0.4: Add actual counts/cpms for samples from a table.

• Version 0.5: Translate sample names with translation table.