# HG changeset patch # User luca_milaz # Date 1724963510 0 # Node ID 978a883ab2f4942002e9d6d9c2831fc59190b7ca # Parent 9f5db0e377a67a3a56b9758f423773e372429ab6 Uploaded diff -r 9f5db0e377a6 -r 978a883ab2f4 marea_2/flux_to_map.xml --- a/marea_2/flux_to_map.xml Thu Aug 29 20:24:59 2024 +0000 +++ b/marea_2/flux_to_map.xml Thu Aug 29 20:31:50 2024 +0000 @@ -144,17 +144,17 @@ What it does ------------- -This tool analyzes and visualizes differences in reactions fluxes of groups of samples, returned by the Flux Simulation tool, of groups of samples. +This tool analyzes and visualizes differences in reactions fluxes of groups of samples returned by the Flux Simulation tool. Accepted files are: - option 1) two or more fluxes datasets, each referring to samples in a given group. The user can specify a label for each group; - option 2) one fluxes dataset and one group-file specifying the group each sample belongs to (e.g. the accepted group file is thought to be the one returned by the Clustering tool). Optional files: - - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example. + - custom svg map. Graphical elements must have the same IDs of reactions. The tool generates: - - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes; + - 1) a tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes; - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes; - 3) a log file (.txt). @@ -170,12 +170,12 @@ Example input ------------- -"RAS of group 1 + RAS of group 2 + ... + RAS of group N" option: +"Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N" option: -RAS Dataset 1: +Fluxes Dataset 1: +------------+----------------+----------------+----------------+ -| Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 | +| Reaction ID| Patient1 | Patient2 | Patient3 | +============+================+================+================+ | r1642 | 0.523167 | 0.371355 | 0.925661 | +------------+----------------+----------------+----------------+ @@ -188,10 +188,10 @@ | r1646 | 0.876543 | 0.786543 | 0.897654 | +------------+----------------+----------------+----------------+ -RAS Dataset 2: +Fluxes Dataset 2: +------------+----------------+----------------+----------------+ -| Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 | +| Reaction ID| Patient1 | Patient2 | Patient3 | +============+================+================+================+ | r1642 | 0.523167 | 0.371355 | 0.925661 | +------------+----------------+----------------+----------------+ @@ -204,12 +204,12 @@ | r1646 | 0.876543 | 0.786543 | 0.897654 | +------------+----------------+----------------+----------------+ -"RAS of all samples + sample group specification" option: +"Fluxes of all samples + sample group specification" option: -RAS Dataset: +Fluxes Dataset: +------------+----------------+----------------+----------------+ -| Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 | +| Reaction ID| Patient1 | Patient2 | Patient3 | +============+================+================+================+ | r1642 | 0.523167 | 0.371355 | 0.925661 | +------------+----------------+----------------+----------------+ @@ -227,11 +227,11 @@ +---------------+-----------+ | Patient ID | Class | +===============+===========+ -| TCGAAA3529 | MSI | +| Patient1 | 0 | +---------------+-----------+ -| TCGAA62671 | MSS | +| Patient2 | 1 | +---------------+-----------+ -| TCGAA62672 | MSI | +| Patient3 | 1 | +---------------+-----------+ @@ -239,8 +239,6 @@ .. class:: infomark -**TIP**: This tool using the RAS scores computed by `Ras tool`_. - ]]>