Commit 02d02eb6 authored by svolant's avatar svolant
Browse files

Couleur barplot pca/pcoa + correction bug correlation

parent 1b2e73dc
...@@ -402,7 +402,11 @@ PCoAPlot_meta <-function (input, dds, group_init, col = c("SpringGreen","dodgerb ...@@ -402,7 +402,11 @@ PCoAPlot_meta <-function (input, dds, group_init, col = c("SpringGreen","dodgerb
s.class(dfxy = pco.counts.norm$li, fac = group, col = col, label = levels(group), add.plot = TRUE, cpoint = 0, clabel = 0, cstar = input$cexstar, cell=input$cexcircle) s.class(dfxy = pco.counts.norm$li, fac = group, col = col, label = levels(group), add.plot = TRUE, cpoint = 0, clabel = 0, cstar = input$cexstar, cell=input$cexcircle)
} }
}else{ }else{
barplot(eigen[1:7], xlab="Dimensions", ylab="Eigenvalues (%)", names.arg = 1:7, col = c(rep("black", 2), rep("grey", 5)), ylim=c(0,max(eigen)+5), cex.axis=1.2, cex.lab=1.4,cex.names=1.2) v_axes = c(as.numeric(gsub("PC","",input$PCaxe1)),as.numeric(gsub("PC","",input$PCaxe2)))
nbBar = max(7,max(v_axes))
col = rep("grey",nbBar)
col[v_axes] = "black"
barplot(eigen[1:nbBar], xlab="Dimensions", ylab="Eigenvalues (%)", names.arg = 1:nbBar, col = col, ylim=c(0,max(eigen)+5), cex.axis=1.2, cex.lab=1.4,cex.names=1.2)
} }
} }
...@@ -474,7 +478,12 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))), ...@@ -474,7 +478,12 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
text(pca$x[, as.numeric(gsub("PC","",input$PCaxe1))] - ifelse(pca$x[, as.numeric(gsub("PC","",input$PCaxe1))] > 0, abs, -abs), pca$x[,as.numeric(gsub("PC","",input$PCaxe2))] - ifelse(pca$x[,as.numeric(gsub("PC","",input$PCaxe2))] > 0, ord, -ord), colnames(counts.trans), col = col[indgrp],cex=input$cexLabelDiag) text(pca$x[, as.numeric(gsub("PC","",input$PCaxe1))] - ifelse(pca$x[, as.numeric(gsub("PC","",input$PCaxe1))] > 0, abs, -abs), pca$x[,as.numeric(gsub("PC","",input$PCaxe2))] - ifelse(pca$x[,as.numeric(gsub("PC","",input$PCaxe2))] > 0, ord, -ord), colnames(counts.trans), col = col[indgrp],cex=input$cexLabelDiag)
} }
if(plot=="eigen"){eigen = pca$sdev[1:min(7,ncol(counts.trans))]^2; barplot(eigen, xlab="Dimensions", ylab="Eigenvalues (%)", names.arg = 1:min(7,ncol(counts.trans)), col = c(rep("black", 3), rep("grey", 4)), ylim=c(0,max(eigen)+5), cex.axis=1.2, cex.lab=1.4,cex.names=1.2)} if(plot=="eigen"){
nbBar = max(7,max(c(as.numeric(gsub("PC","",input$PCaxe1)),as.numeric(gsub("PC","",input$PCaxe2)))))
col = rep("grey",nbBar)
eigen = pca$sdev[1:nbBar]^2
col[c(as.numeric(gsub("PC","",input$PCaxe1)),as.numeric(gsub("PC","",input$PCaxe2)))] = "black"
barplot(eigen, xlab="Dimensions", ylab="Eigenvalues (%)", names.arg = 1:nbBar, col = col, ylim=c(0,max(eigen)+5), cex.axis=1.2, cex.lab=1.4,cex.names=1.2)}
} }
} }
......
...@@ -292,7 +292,7 @@ Plot_Visu_Scatterplot<- function(input,resDiff,export=FALSE,lmEst = FALSE,CorEst ...@@ -292,7 +292,7 @@ Plot_Visu_Scatterplot<- function(input,resDiff,export=FALSE,lmEst = FALSE,CorEst
if(any(numInd)) data = cbind(target[,numInd],log2(t(counts)+1),div) if(any(numInd)) data = cbind(target[,numInd],log2(t(counts)+1),div)
if(!any(numInd)) data = cbind(log2(t(counts)+1),div) if(!any(numInd)) data = cbind(log2(t(counts)+1),div)
cor.est = cor(as.matrix(data),method = input$CorMeth,na.rm=TRUE) cor.est = round(cor(as.matrix(data),method = input$CorMeth),3)
#cor.pvalue = cor.test(data,method = input$CorMeth) #cor.pvalue = cor.test(data,method = input$CorMeth)
return(list(cor.est=cor.est)) return(list(cor.est=cor.est))
} }
......
...@@ -24,7 +24,7 @@ shinyServer(function(input, output,session) { ...@@ -24,7 +24,7 @@ shinyServer(function(input, output,session) {
## Counts file ## Counts file
dataInputCounts <-reactive({ dataInputCounts <-reactive({
print(input$TypeTaxo)
inFile <- input$fileCounts inFile <- input$fileCounts
if (is.null(inFile)) return(NULL) if (is.null(inFile)) return(NULL)
......
...@@ -346,7 +346,7 @@ body <- dashboardBody( ...@@ -346,7 +346,7 @@ body <- dashboardBody(
conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='SERE' || input.DiagPlot=='clustPlot' ", conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='SERE' || input.DiagPlot=='clustPlot' ",
selectInput("DistClust","Distance",c("euclidean", "SERE"="sere", "canberra", "bray", "kulczynski", "jaccard", selectInput("DistClust","Distance",c("euclidean", "SERE"="sere", "canberra", "bray", "kulczynski", "jaccard",
"gower", "altGower", "morisita", "horn","mountford","raup","binomial", "gower", "altGower", "morisita", "horn","mountford","raup","binomial",
"chao","cao","mahalanobis"),selected="jaccard") "chao","cao","mahalanobis"),selected="canberra")
) )
......
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