Change the way to follow the app

libraries_updates.R

-#### to avoid conflict between d3heatmap and rnvd3 #####
-# the conflict come from the fact that both libraries use d3 but not the same version
-# when the most recent one is loaded (the one of d3heatmap), it breaks the one of rNVD3
-# the idea here is to modify the d3 of d3heatmap so that the library create an object called d33
-# then modify the d3heatmap files so that it use this d33 object instead of d3
-
-# first get d3heatmap javascript library path
-d3heatmap_path = paste(.libPaths(), 'd3heatmap/htmlwidgets/lib/', sep='/')
-
-# then get all js files in this directory
-js_files = dir(path=d3heatmap_path, pattern = "*.js$", recursive = T, full.names = T)
-
-# then create a function tu update the files
-d3_to_d33 = function(target){
-  # the function will use the bash tool sed on the file target
-  # it makes 3 replacements
-  system(command=paste('sed -i .bck -e "s/d3\\ /d33 /g" -e "s/d3\\./d33./g" -e "s/d3;/d33;/g" ', target))
-}
-# apply the replacement function to all js files
-sapply(js_files, d3_to_d33)
-
-# change from d3.min.js to d3.js in the yaml file
-system(command=paste('sed -i .bck -e "s/d3\\.min/d3/g" ', .libPaths(), '/d3heatmap/htmlwidgets/d3heatmap.yaml', sep=''))
-
-# it's done. d3heatmap should use d33 object now
-
-#### replacement of the css cals of the rNVD3 ####
-
-# get the rNVD3 path
-#rNVD3_path = paste(.libPaths(), 'rNVD3/nvd3/css/', sep='/')
-
-# get the path of the current source. may need to be modified (parent.frame(1) or parent.frame(2) or parent.frame(3) or else) 
-#current_path = dirname(parent.frame(2)$ofile) 
-# get the css files path
-#css_files = dir(path=current_path, pattern = "*.css$", full.names = T)
-# create the function to copy the css file
-#cp_to_rNVD3 = function(p, dest){
-#  system(paste('cp', p, dest))
-#}
-#apply the copy to all the css files
-#sapply(css_files, cp_to_rNVD3, rNVD3_path)
-
-# first get d3heatmap javascript library path
-scatterD3_path = paste(.libPaths(), 'scatterD3/htmlwidgets/', sep='/')
-
-# then get all js files in this directory
-js_files = dir(path=scatterD3_path, pattern = "*.js$", recursive = T, full.names = T)
-
-# then create a function tu update the files
-d3_to_d333 = function(target){
-  # the function will use the bash tool sed on the file target
-  # it makes 3 replacements
-  system(command=paste('sed -i .bck -e "s/d3\\ /d333 /g" -e "s/d3\\./d333./g" -e "s/d3;/d333;/g" -e "s/d3=/d333=/g" ', target))
-}
-# apply the replacement function to all js files
-sapply(js_files, d3_to_d333)
-
-# change from d3.min.js to d3.js in the yaml file
-system(command=paste('sed -i .bck -e "s/d3$/d333/g" ', .libPaths(), '/scatterD3/htmlwidgets/scatterD3.yaml', sep=''))
-

ui.R

@@ -71,7 +71,8 @@ body <- dashboardBody(
             div(style="width:100% ; max-width: 1200px; height: 550px",
                 
               tabBox(title="Welcome to SHAMAN", id="tabset1", width=NULL,
-                   tabPanel("About", tags$script(type="text/javascript", language="javascript", src="google-analytics.js"),
+                   # tags$script(type="text/javascript", language="javascript", src="google-analytics.js"),
+                   tabPanel("About", 
                             p("SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization,
                                        the differential analysis and mutiple visualization.",style = "font-family: 'times'; font-si16pt"),
                             p("SHAMAN is based on DESeq2 R package", a("[Anders and Huber 2010]", href="http://www.ncbi.nlm.nih.gov/pubmed/20979621"), "for the analysis of metagenomic data, as suggested in", a("[McMurdie and Holmes 2014,",href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/"),a("Jonsson2016]",href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/"),

www/google-analytics.js

-  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-  ga('create', 'UA-72614324-2', 'auto');
-  ga('send', 'pageview');