Examine your omics datasets in the prior knowledge context.
Follow the steps as indicated in interactive menu.
For the help overlay the mouse over the info button or go to Quick help section.
Large knowledge networks of Arabidopsis thaliana and Solanum tuberosum immune signalling are provided.
ππ ZagorΕ‘Δak, M., Blejec, A., RamΕ‘ak, Ε½. et al. DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R. Plant Methods 14, 78 (2018). https://doi.org/10.1186/s13007-018-0345-0
π https://omictools.com/dinar-tool (obsolete)
π¦ http://isbe.si/2018/09/04/dinar-article-published-in-plant-methods/
π¦ https://www.facebook.com/NIBSlovenia/videos/318025485411839/
sudo apt-get install r-base
sudo apt-get install r-base-dev
sudo apt-get -y install libcurl4-gnutls-dev
sudo apt-get -y install libssl-dev
sudo apt-get install libv8-dev
if (!require("devtools")) install.packages("devtools")
if (!require('Rcpp')) install.packages('Rcpp')
devtools::install_github("rstudio/shiny")
install.packages("shiny", dependencies=TRUE)
install.packages("devtools", lib="~/R/lib")
shiny:::runGitHub("DiNAR", "NIB-SI", subdir = "DiNARscripts/")
*Note: this will install/load libraries: (V8), igraph, colourpicker, plotly, ggplot2, calibrate, stringi, magrittr, yaml, animatoR, stringr, wordcloud2, shinyjs, shinydashboard, shinyBS, colorspace, knitr, markdown, Rcpp, dplyr, rdrop2, fBasics, shinyIncubator, shinysky, downloader, visNetwork, htmltools, htmlwidgets, intergraph, network, ndtv, shinyFiles and pryr
π https://NIB-SI.shinyapps.io/DiNAR (Basic - Performance Boost; Instance Size: 8GB; Max Worker Processes: 10; Max Connections per Worker: 1; Max Instances: 3)
- download zip and run locally in RStudio: https://www.rstudio.com/products/rstudio/download/#download https://shiny.rstudio.com/tutorial/
- download zip and deploy: http://shiny.rstudio.com/articles/shinyapps.html http://shiny.rstudio.com/articles/scaling-and-tuning.html
- download zip and https://support.rstudio.com/hc/en-us/articles/214771447-Shiny-Server-Administrator-s-Guide
http://conferences.nib.si/DiNAR/
- in animatedPlotAB.R uncomment lines:
subDir <- "./plots"
dir.create(file.path(subDir), showWarnings = FALSE)
myfilename = paste0("SampleGraph", length(list.files(subDir))+1, '.pdf')
myfilepath = file.path(subDir)
par(mai=c(2.0, 2.0, 2.0, 2.0))`
and
dev.copy2pdf(file = paste0(myfilepath, '/', myfilename), width=24, # height=18, out.type="pdf")
- install LaTeX (e.g. https://miktex.org/) or use overleaf
- install animate Package
- copy to working directory and run LaTeX template document: CreatePDFanimation.tex (for more details see this)
- in animatedPlotAB.R uncomment few lines below
# To generate .pdf animation
comment - replace
myfilename = paste0("SampleGraph", length(list.files(subDir))+1, '.pdf')
withmyfilename = paste0("SampleGraph", formatC(length(list.files(subDir))+1, width=4, flag="0"), '.png')
- add few lines of code before
newplot
to save all produced images in .png format; e.g.
dev.copy(device = png,
filename = paste0(myfilepath, '/', myfilename),
width = 1500, height = 1500,
units = "px", pointsize = 12)
add dev.off()
at the end of the function- run short python2 script containing the following code (take care of dependencies!):
import imageio
import os
with imageio.get_writer('./my.gif', mode='I') as writer:
for filename in sorted(os.listdir("./images/")): # images == myfilepath == where .png images of interest are
filename="./images/"+filename
print(filename)
image = imageio.imread(filename)
writer.append_data(image)
Find more information at: https://rfunction.com/archives/812 and https://imageio.github.io/
- input pre-processing: π https://github.com/NIB-SI/DiNAR/tree/master/subApps/pre-processing (π https://nib-si.shinyapps.io/pre-processing/)
- network clustering: π https://github.com/NIB-SI/DiNAR/tree/master/subApps/clustering (π https://nib-si.shinyapps.io/clustering/)
- shortestPaths: π https://github.com/NIB-SI/DiNAR/tree/master/subApps/shortestPaths
- CustomNetwork from GMM-KnetMiner-SKM combo: π¦ https://github.com/NIB-SI/DiNAR/tree/master/subApps/GMM-SKM-KnetMiner (π¦ https://nib-si.shinyapps.io/GMM-SKM-KnetMiner/)
π₯ https://github.com/NIB-SI/DiNAR/tree/master/GEODataAnalysis
- π¦ Plant Data Visualization/Orthology Bundle - Cork Oak Use Case
- π¦ FAIR Data-finder for Agronomic Research (FAIDARE)
- skm.nib.si
- knetminer.com
- gomapman.nib.si
- org.At.tair.db - Genome wide annotation for Arabidopsis
- AraCyc
- PLAZA
- STRING
- Ath Interactome
- ATRM: Arabidopsis Transcriptional Regulatory Map
- Cytoscape
https://github.com/NIB-SI/DiNAR/tree/master/NetworkClustering
(*) UnicodePlus