Commit 956df065 authored by svolant's avatar svolant
Browse files

Shinydashboard css

parent f6f30bc1
......@@ -8,7 +8,7 @@ if(!require(shiny)){
library(shiny)
}
if(!require(shinydashboard)){
install.packages('shinydashboard')
devtools::install_github('aghozlane/shinydashboard')
library(shinydashboard)
}
......
......@@ -341,12 +341,13 @@ PCoAPlot_meta <-function (input, dds, group_init, col = c("SpringGreen","dodgerb
if(input$CountsType=="Normalized") counts.norm = as.data.frame(round(counts(dds, normalized = TRUE)))
# was removed
counts.norm = counts.norm[,ind_kept]
print(head(counts.norm))
# print(head(counts.norm))
## Get the distance
if(input$DistClust!="sere") dist.counts.norm = vegdist(t(counts.norm), method = input$DistClust)
if(input$DistClust=="sere") dist.counts.norm = as.dist(SEREcoef(counts.norm))
# save(counts.norm,dist.counts.norm,file="testNMDS.RData")
## Do PCoA
pco.counts.norm = dudi.pco(d = dist.counts.norm, scannf = FALSE,nf=ncol(counts.norm))
......@@ -687,8 +688,11 @@ NMDSPlot <-function (input, dds, group_init, col = c("SpringGreen","dodgerblue",
if(input$DistClust=="sere") dist.counts.norm = as.dist(SEREcoef(counts.norm))
## Do PCoA
pco.counts.norm = dudi.pco(d = dist.counts.norm, scannf = FALSE,nf=ncol(counts.norm))
## Do NMDS
nmds.counts.norm = metaMDS(dist.counts.norm,k=round(ncol(counts.norm)/2), trymax = 25)
dudi.pco(d = dist.counts.norm, scannf = FALSE,nf=ncol(counts.norm))
## Get eigen values
eigen=(pco.counts.norm$eig/sum(pco.counts.norm$eig))*100
......
......@@ -14,9 +14,10 @@ if (!require(scatterD3)) {
library(scatterD3)
}
if(!require(shinydashboard)){
installed.packages("shinydashboard")
library(shinydashboard)
devtools::install_github('aghozlane/shinydashboard')
library(shinydashboard)
}
if(!require(shinythemes)){
install.packages("shinythemes")
library(shinythemes)
......
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