Commit cdddde0a authored by Perrine Woringer's avatar Perrine Woringer
Browse files

Debug clustering and pca, plus some cometics

parent 8c8b8e19
......@@ -66,11 +66,11 @@ if(!require(treeWeightD3)){
devtools::install_github('pierreLec/treeWeightD3')
library(treeWeightD3)
}
if (!require(BiocInstaller)){
source("https://bioconductor.org/biocLite.R")
biocLite("BiocInstaller")
library(BiocInstaller)
}
# if (!require(BiocInstaller)){
# source("https://bioconductor.org/biocLite.R")
# biocLite("BiocInstaller")
# library(BiocInstaller)
# }
if (!require(d3heatmap)) {
devtools::install_github('aghozlane/d3heatmap')
......@@ -263,3 +263,8 @@ if(!require("visNetwork")){
install.packages("visNetwork")
library(visNetwork)
}
if(!require("SummarizedExperiment")){
BiocManager::install("SummarizedExperiment")
library(SummarizedExperiment)
}
\ No newline at end of file
......@@ -138,7 +138,7 @@ HCPlot <- function (input,dds,group,type.trans=NULL,counts=NULL,CT,tree,col = c(
## Get the type of dendrogram
type <- input$typeHculst
dend <- set(dend, "labels_cex", input$cexLabelDiag)
#dend <- set(dend, "labels_cex", input$cexLabelDiag)
if(input$colorHC) labels_colors(dend)<-col[as.integer(as.factor(group))][order.dendrogram(dend)]
if(type=="hori")
{
......@@ -148,7 +148,8 @@ HCPlot <- function (input,dds,group,type.trans=NULL,counts=NULL,CT,tree,col = c(
else
{
par(cex=input$cexTitleDiag,mar=c(6,6,4,5))
res = circlize_dendrogram(dend, labels_track_height = 0.2, dend_track_height = .3, main = "Cluster dendrogram",xlab = paste(input$DistClust,"distance, Ward criterion",sep=" "))
res = circlize_dendrogram(dend, labels_track_height = 0.2, dend_track_height = .3, main = "Cluster dendrogram",xlab = paste(input$DistClust,"distance, Ward criterion",sep=" "),
labels_cex = input$cexLabelDiag)
}
}
}
......@@ -554,8 +555,8 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
{
type.trans <- type.trans[1]
if (type.trans == "VST") counts.trans <- assay(varianceStabilizingTransformation(dds))
else counts.trans <- assay(rlogTransformation(dds))
if (type.trans == "VST") counts.trans <- SummarizedExperiment::assay(varianceStabilizingTransformation(dds))
else counts.trans <- SummarizedExperiment::assay(rlogTransformation(dds))
counts.trans = counts.trans[,ind_kept]
rv = apply(counts.trans, 1, var, na.rm = TRUE)
......@@ -754,8 +755,8 @@ Get_pca_table <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
{
type.trans <- type.trans[1]
if (type.trans == "VST") counts.trans <- assay(varianceStabilizingTransformation(dds))
else counts.trans <- assay(rlogTransformation(dds))
if (type.trans == "VST") counts.trans <- SummarizedExperiment::assay(varianceStabilizingTransformation(dds))
else counts.trans <- SummarizedExperiment::assay(rlogTransformation(dds))
counts.trans = counts.trans[,ind_kept]
rv = apply(counts.trans, 1, var, na.rm = TRUE)
......
......@@ -1234,7 +1234,7 @@ function(request) {
),
column(width=3,
box(title = "Select your plot", width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
selectizeInput("PlotVisuSelectComp","",c("Venn diagram"="Venn","Heatmap"="Heatmap_comp", "Logit plot"="LogitPlot", "p value density"="pValueDensity", "UpSet"="UpSet", "Multiple venn compair" = "multipleVenn"),selected = "Heatmap_comp")
selectizeInput("PlotVisuSelectComp","",c("Venn diagram"="Venn", "UpSet"="UpSet", "Contrasts compair" = "multipleVenn" ,"Heatmap"="Heatmap_comp", "Logit plot"="LogitPlot", "Density plot"="pValueDensity"),selected = "Heatmap_comp")
),
box(title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
conditionalPanel(condition="input.PlotVisuSelectComp=='Heatmap_comp' || input.PlotVisuSelectComp=='UpSet' || input.PlotVisuSelectComp=='pValueDensity' || input.PlotVisuSelectComp=='multipleVenn'",
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment