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All the scripts are distributed under GPL v3 licence.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

===================================================================================================================
Data and scripts contained in this archive are part of the study:

Inglese et al. "Analysis of colocalised metabolite signals from colorectal cancer DESI mass spectrometry imaging
data associated with metastatic recurrence"

Folder structure:

\- data_10cm (DESI imaging data from specimens collected at 10cm from the tumour centre.
	      Each subfolder is associated with a patient.
              The X_preprocessed.RData contains the intensity matrix (rows = pixels, cols = ions),
              preprocessed with median scaling and log(x + 1) transformation. The common m/z vector
              values are represented in the columns name. The image_size.RData contains the spatial
              dimensions (pixels x pixels) of the MS image.)

\- data_centre (DESI imaging data from specimens collected in the tumour centre.
		Each subfolder is associated with a patient.
                The X_preprocessed.RData contains the intensity matrix (rows = pixels, cols = ions),
                preprocessed with median scaling and log(x + 1) transformation. The common m/z vector
                values are represented in the columns name. The image_size.RData contains the spatial
                dimensions (pixels x pixels) of the MS image.)

\- R scripts (All the R language scripts used to reproduce the network analysis and the figures.
              The numeric value before each filename indicates the order of execution.)
    \- functions (Support functions for the entire workflow.)
    \- script_for_figures (R scripts used to reproduce the figures. These can be run after the main folder
                           scripts have been run.)

\- results_10cm (All the results of the network analysis regarding the samples at 10cm from the tumour centre.)
    \- met (Results associated with the patients with a metastatic recurrence.)
    \- non-met (Results associated with the patients without a metastatic recurrence.)

\- results_centre (All the results of the network analysis regarding the samples from the tumour centre.)
    \- met (Results associated with the patients with a metastatic recurrence.)
    \- non-met (Results associated with the patients without a metastatic recurrence.)

====================================================================================================================
All the scripts are written in R language and have been tested with R 3.4.2 on Windows 10.

The user must set the WORK_DIR (the directory containing all the data and scripts.)
When present, the global variables STUDY and DATASET must be set accordingly with the required analysis.

STUDY: "centre" (Analysis of the tumour centre samples)
       "10cm" (Analysis of the samples at 10cm from the tumour)

DATASET: "met" (Analysis of the patients with a metastatic recurrence)
         "non-met" (Analysis of the patients without a metastatic recurrence)