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License: GNU General Public License v3.0

R 72.02% Shell 0.04% CSS 6.06% JavaScript 12.42% Python 0.14% PostScript 3.75% HTML 5.56%

shiny shiny-server r transcriptomics css html chipseq heatmap pca venn-diagram

ma_trix_app's Introduction

MATRiX is a shiny application for Mining and functional Analysis of TRanscriptomics data.

Introduction
Installation
Contact
Acknowledgements

Introduction

This project initiate by Yannick Lippi aims to facilitate access to biologists in order to publish graphs such as heatmap, PCA or Venn diagram related to transcriptomic data. MATRiX is an application dedicated to DNA chip, RNA-seq and ChIP-Seq analysis, this application incorporates quality control with Principal components analysis helping to summarize the data and differential analysis with various methods such as Venn diagram, Heatmap clustering and GO Enrichment analysis by querying the DWS (DAVID WEB SERVICES).

MATRiX app is working with specific data produced by the limma, DESeq2, edgeR packages, resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995]. PCA is computed with the FactoMineR package and the plot is produced with the factoextra package, for the Heatmap and Venn diagram the graphs are obtained respectively with the gplots and VennDiagram package, those packages are available on CRAN This application works only with specific data, you can check the example file (MA_Trix_App/downloadData.zip)

Here's the global workflow passing by the experiment to the visualization:

and also a video Presentation

Installation

MATRiX is available for R>3.5.0. The installation, download and execution can all be performed with a small R script : First you'll need to install RJava in the aim to using RDAVIDWebService. You can install it using the following commands:

sudo apt-get install default-jdk
sudo R CMD javareconf #to associate it with R
sudo apt-get install r-cran-rjava
sudo apt-get install libgdal1-dev libproj-dev
sudo apt-get install libv8-3.14-dev

## Install RDAVIDWebService into R
source("https://bioconductor.org/biocLite.R")
biocLite("RDAVIDWebService")
install.packages("rJava")

## Load RDAVIDWebService
library(RDAVIDWebService)

## Load shiny packages
if(!require('shiny')){
 install.packages('shiny')
 library(shiny)
}

# Install dependencies, download last version of MATRiX from github and run matrix in one command :
runGitHub('GeT-TRiX/MA_Trix_App')

If RDAVIDWebService and Shiny are installed on your machine can also run the app as following :

git clone https://github.com/GeT-TRiX/MA_Trix_App
chmod +x ./cmd.sh
./cmd.sh

Contact

Here are our mail [Franck Soubès] ([email protected]) or [Yannick Lippi] ([email protected]) for any questions, suggestions or if you need help to use MATRiX, dont hesitate to contact us.

Acknowledgements

The main contributors to MATRiX:

Yannick Lippi, (Initiator, beta-testing, feature suggestions),

Franck Soubès, (Coding, Unit testing, documentation, packaging, feature suggestions),

Didier Laborie, (Virtual machine and DNS),

TOXALIM Team: BioToMyc & TIM, (beta-testing, feature suggestions)

Claire Naylies, (suggestions)

ma_trix_app's People

Contributors

Stargazers

Watchers

ma_trix_app's Issues

Error in Enricher api

when sending gene list from heatmap to enricher this gives a blank page with this content:
{
"expired": true
}

StripChart: change samples naming

sampleNames are renamed to get only numbers, pasted with groupName. this can generate duplicated sampleNames and ERROR.
Solution: Disable sample name renaming

stripChart lost grouping by condition

StripChart: Add log2 to y axis name

confusion in y axis name. Data are log2 expression values.
Solution: rename yaxis to "log2 expression"

Adpat Color choices

Il serait bien qu'il y ait la possibilité de choisir parmi toutes les couleurs possibles afin d'obtenir des figure cohérentes avec nos résultats obtenus via d'autre logiciel

enlarge filter criteria for stripchart

in stripchart, enlarge pvalue criteria to have the possibility to highlight non regulated genes.

correct FCthreshold in volcano

the FC treshold in volcano plot is based on log2FC.
Correct this to be based on FC
->file function/EnhancedVolcano.R

Functional analysis

Review the Functional analysis widget of Heatmap:
line 1: Organism[list]; category[list]
line 2: Run Enrichment Analysis[buton]; with DAVID WS[text]
line 3: Send to DAVID[button]; Cluster[list]

manage NA values in ResTable

Sometimes, ResTables can contain NA values in FC, pvalues... and causes error in summary table, stripChart and heatmap.
2 possible solutions:
Choice 1 - manage NA values in summary page, heatmapand StripChart filtering criteria.
Choice 2 - filter out lines with NA after data loading

clear unnecessary files

some files are not necessary for the app to run.
final

Send Heatmap cluster to String.db?

here the strategy:
https://string-db.org/help//api/#embedding-the-interactive-network

integration to shiny:
https://stackoverflow.com/questions/60492135/string-interactive-network-in-shiny-in-r
https://www.semicolonworld.com/question/66144/string-interactive-network-in-shiny-in-r

lost rownames in heatmap clusters summary table

data stored in grouplength object (server/HeatmapHiny.R).
solution: transform rowname to column.

Enhance heatmap data export

Suggestion from annual satisfaction survey:
"Pouvoir extraire les logFC mais aussi les p-values et les p-values corrigées à partir des sous-groupes de gènes identifiés dans un cluster "
-> add logFC and Pval to the "Table summarizing the heatmap" in "Clusters" tab of Heatmap Menu.

Failure in sending heatmap gene list to DAVID api

got this msg:
Due to the ambiguous nature of gene symbols, DAVID does not allow their upload with the API at this time.
We are currently developing methods to submit a taxonomy id with an api call for OFFICIAL_GENE_SYMBOL.
Please Contact Us if you have any questions.

-> update the kind of gene identifiers used for the request

Error in volvanoplot eps export

when on wants to save a volcano to eps file, it exports the last plot generated (barplot).
Origin: /module/savemodules.R:L#116
Cause: ggsave by default save the lsat plot object generated, so the barplot if it is generated.
Solution: change the use of command ggsave() to cairo_ps()

button name in volcanoplot/barplot

names of export push buttons are inverted in volcano page
solution: revert the names of export buttons