Commit 1b8184c1 authored by Bagueneau Mathias's avatar Bagueneau Mathias
Browse files

- Gene page : GO avec Dotplot possible selon le group et le facteur

parent fde9160a
......@@ -33,7 +33,7 @@ https://gitlab.univ-nantes.fr/E176261N/singlecell
Here the list of the required packages for Shiny SChnurR :
* [Shiny][Shiny]
* [Seurat][Seurat] : **The version 3 is required !**
* [Seurat][Seurat]
* [SCTransform][Sctransform]
* shinythemes
* dplyr
......@@ -53,7 +53,7 @@ Here the list of the required packages for Shiny SChnurR :
* org.Hs.eg.db
* tools
All of this packages are installed with the provided script **install.R**.
All of this packages are installed with the provided script **install.R** and are up-to-date.
# - Tutorial
......
......@@ -18,12 +18,14 @@ library(data.table)
library(clusterProfiler)
library(org.Hs.eg.db)
library(tools)
library(PANTHER.db)
# library(topGO)
# library(BiocGenerics)
# library(GO.db)
# library(DOSE)
# library(PANTHER.db)
### ----------------------------- User interface -----------------------------------------------------
......@@ -72,7 +74,8 @@ sidebar <- dashboardSidebar(
verbatimTextOutput(outputId = "no_file2"),
conditionalPanel(condition= "output.fileUploaded",align="center",
uiOutput("fchoice4"), br(),
uiOutput("group"), br(),
uiOutput("group"), br(),
radioButtons("gographtype", label="Choose a graph type :", choices=c("Dotplot"="dplot", "Barplot"="bplot", "Emapplot" = "eplot")), br(),
br(), actionButton("gogo", icon = icon("far fa-arrow-alt-circle-right"), label="Do Gene Ontology")
)
)
......@@ -440,7 +443,14 @@ server <- function(input, output, session) {
OrgDb = org.Hs.eg.db,
drop = TRUE)
ego <- withProgress(enrichGO(gene = genes$ENTREZID, OrgDb = "org.Hs.eg.db", keyType= "ENTREZID", ont = "BP", readable = TRUE), message = "Loading Gene Ontology...", value=1)
dotplot(ego)
if (input$gographtype == "dplot") {
dotplot(ego)
} else if (input$gographtype == "bplot") {
barplot(ego, drop=TRUE)
} else {
emapplot(ego)
}
})
output$goplot <-renderPlot ({
......
......@@ -22,4 +22,6 @@ install.packages("BiocManager")
devtools::install_github(repo = 'ChristophH/sctransform')
BiocManager::install("clusterProfiler")
BiocManager::install("MAST")
BiocManager::install("org.Hs.eg.db")
\ No newline at end of file
BiocManager::install("org.Hs.eg.db")
BiocManager::install("PANTHER.db")
# BiocManager::install("topGO")
\ No newline at end of file
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