Commit cf38c158 authored by Bagueneau Mathias's avatar Bagueneau Mathias
Browse files

- Ajouts de logos

- Suppression des jeux de données obsolètes
parent c9ada034
...@@ -230,10 +230,14 @@ body <- dashboardBody( ...@@ -230,10 +230,14 @@ body <- dashboardBody(
p("IRS-UN"), p("IRS-UN"),
p("8 Quai Moncousu"), p("8 Quai Moncousu"),
p("44007 Nantes"), br(), p("44007 Nantes"), br(),
img(src = "crcina.png", height = 180, width = 400, align="center"), br(),
fluidPage( fluidPage(
column(width=6, img(src = "hema.png", height = 100, width = 300, align="center")), column(width=4, img(src = "hema.png", align="center")),
column(width=6, img(src = "siric.jpg", height = 180, width = 180, align="center"))), column(width=4, img(src = "crcina.png", align="center")),
column(width=4, img(src = "sysmics.png", height = 100, align="center"))), br(),
fluidPage(
column(width=4, img(src = "univ.png", height = 150, align="center")),
column(width=4, img(src = "chu.png", height = 150, align="center")),
column(width=4, img(src = "siric.jpg", height = 100, align="center"))),
br(), hr(), br(), p(em("Development Team : Jean-Baptiste ALBERGE, Jonathan CRUARD, Mathias BAGUENEAU"), br(), em("Beta-test : Benjamin DELAUNE")), br(), hr(), br(), p(em("Development Team : Jean-Baptiste ALBERGE, Jonathan CRUARD, Mathias BAGUENEAU"), br(), em("Beta-test : Benjamin DELAUNE")),
br(), p(strong("Git repository :"),a(href="https://gitlab.univ-nantes.fr/MathBgn/myelome", "Shiny SChnurR"), br(), em("A complete tutorial is available at this adress.")) br(), p(strong("Git repository :"),a(href="https://gitlab.univ-nantes.fr/MathBgn/myelome", "Shiny SChnurR"), br(), em("A complete tutorial is available at this adress."))
) )
...@@ -844,48 +848,48 @@ server <- function(input, output, session) { ...@@ -844,48 +848,48 @@ server <- function(input, output, session) {
## Help messages -------- ## Help messages --------
observeEvent (input$help1, { observeEvent (input$help1, {
showModal(modalDialog("You first need to upload a .rds file, or choose one already provided as example. showModal(modalDialog("You first need to upload a .rds file, or choose one already provided as example.
Then, many information are provided : Then, many information are provided :
Some files information, with genes and cells number, and the assay used. Some files information, with genes and cells number, and the assay used.
Two graphs for the visualization. Two graphs for the visualization.
A data table with some pre-calculated markers. A data table with some pre-calculated markers.
The first graph allows you to visualise by all the factors (resolution, idents, ...) of your file. The first graph allows you to visualise by all the factors (resolution, idents, ...) of your file.
The second one is for the features or data (all the genes repartitions, scores, ...). The second one is for the features or data (all the genes repartitions, scores, ...).
The two graphs could be controlled with the panel made for. You have two graph modes : t-SNE or UMAP, and clusters informations for every factors. The two graphs could be controlled with the panel made for. You have two graph modes : t-SNE or UMAP, and clusters informations for every factors.
On the graphs, you could also select some cells, and have the percentage of your selection by the total cell number. On the graphs, you could also select some cells, and have the percentage of your selection by the total cell number.
The data table under the graphs is pre-calculated depending the selected factor. The data table under the graphs is pre-calculated depending the selected factor.
It shows all significant markers, calculated with the test MAST. You could affine your marker research with the filters. It shows all significant markers, calculated with the test MAST. You could affine your marker research with the filters.
All of the outputs are exportable : in .svg for the graphs and in .csv for the table.", title=strong("Vizualisation page Help"), easyClose=TRUE, footer = NULL ) All of the outputs are exportable : in .svg for the graphs and in .csv for the table.", title=strong("Vizualisation page Help"), easyClose=TRUE, footer = NULL )
) )
}) })
observeEvent (input$help2, { observeEvent (input$help2, {
showModal(modalDialog("The Genes page allows you to do a Gene Ontology and have information about genes. showModal(modalDialog("The Genes page allows you to do a Gene Ontology and have information about genes.
You have to choose a factor, group(s) of it, and ontology. Three type of ontology are available : Biological Process, Molecular Function and Cellular Component. You have to choose a factor, group(s) of it, and ontology. Three type of ontology are available : Biological Process, Molecular Function and Cellular Component.
Then you will have a graph (you can also change the graph mode), and two tables. Then you will have a graph (you can also change the graph mode), and two tables.
The first table gives you the list of the genes present in your selection. The first table gives you the list of the genes present in your selection.
The second one gives you the ontology. The second one gives you the ontology.
The Gene Ontology also use the pre-calculated markers for each factors (like the data table from the visualization page and the Heatmap). The Gene Ontology also use the pre-calculated markers for each factors (like the data table from the visualization page and the Heatmap).
All of the outputs are exportable : in .png for the graph and in .csv for the tables.", title=strong("Genes page Help"), easyClose=TRUE, footer = NULL ) All of the outputs are exportable : in .png for the graph and in .csv for the tables.", title=strong("Genes page Help"), easyClose=TRUE, footer = NULL )
) )
}) })
observeEvent (input$help3, { observeEvent (input$help3, {
showModal(modalDialog("In this page, you could compare groups from factors with each other. showModal(modalDialog("In this page, you could compare groups from factors with each other.
You could choose multiple groups, and also add a second factor to filter with. You could choose multiple groups, and also add a second factor to filter with.
Then you could Find the significant markers of your selection. Then you could Find the significant markers of your selection.
Be carefull to not select redondant cells. Be carefull to not select redondant cells.
After this, another option and two text areas appears. The text areas are filled with the top 30 genes upregulated from one condition against the other. These areas are writable (you can add or remove some genes). After this, another option and two text areas appears. The text areas are filled with the top 30 genes upregulated from one condition against the other. These areas are writable (you can add or remove some genes).
Then you could do a gene ontology with these two lists. Then you could do a gene ontology with these two lists.
The results are into two tables. The results are into two tables.
Like the Visualization page, you have a Control panel to change some parameters to the graphs (like graph mode, point size, ...) and choose what you want to see (factors, features, ...). Like the Visualization page, you have a Control panel to change some parameters to the graphs (like graph mode, point size, ...) and choose what you want to see (factors, features, ...).
You could also choose an ontology. You could also choose an ontology.
All of the outputs are exportable : in .svg for the graphs and in .csv for the tables. All of the outputs are exportable : in .svg for the graphs and in .csv for the tables.
You could also export the barcodes of the selected cells, in .csv.", title=strong("Compare page Help"), easyClose=TRUE, footer = NULL ) You could also export the barcodes of the selected cells, in .csv.", title=strong("Compare page Help"), easyClose=TRUE, footer = NULL )
) )
}) })
observeEvent (input$help4, { observeEvent (input$help4, {
showModal(modalDialog("The Heatmap page allows you to do a Heatmap with many parameters. showModal(modalDialog("The Heatmap page allows you to do a Heatmap with many parameters.
You could choose a factor and the number of top genes you want to be shown. You could choose a factor and the number of top genes you want to be shown.
The Heatmap also use the pre-calculated markers for each factors (like the data table from the visualization page). The Heatmap also use the pre-calculated markers for each factors (like the data table from the visualization page).
The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClose=TRUE, footer = NULL ) The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClose=TRUE, footer = NULL )
) )
}) })
...@@ -972,7 +976,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos ...@@ -972,7 +976,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos
}) })
output$dlmarkers_compare <- downloadHandler( output$dlmarkers_compare <- downloadHandler(
filename = function() { filename = function() {
paste0(filedata$name,"_markers_",names(df)[[7]],".csv") paste0(file_path_sans_ext(filedata$name),"_markers_",names(df)[[7]],".csv")
}, },
content = function(file) { content = function(file) {
write.csv(df, file, row.names=FALSE) write.csv(df, file, row.names=FALSE)
...@@ -1007,7 +1011,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos ...@@ -1007,7 +1011,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos
}) })
output$dlonto_compare1 <- downloadHandler( output$dlonto_compare1 <- downloadHandler(
filename = function() { filename = function() {
paste0(filedata$name,"_onto_",input$ontology2,"_datatable_",input$fsel2,".csv") paste0(file_path_sans_ext(filedata$name),"_onto_",input$ontology2,"_datatable_",input$fsel2,".csv")
}, },
content = function(file) { content = function(file) {
write.csv(dfo, file, row.names=FALSE) write.csv(dfo, file, row.names=FALSE)
...@@ -1037,7 +1041,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos ...@@ -1037,7 +1041,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos
}) })
output$dlonto_compare2 <- downloadHandler( output$dlonto_compare2 <- downloadHandler(
filename = function() { filename = function() {
paste0(filedata$name,"_onto_",input$ontology2,"_datatable_",input$fsel2,".csv") paste0(file_path_sans_ext(filedata$name),"_onto_",input$ontology2,"_datatable_",input$fsel2,".csv")
}, },
content = function(file) { content = function(file) {
write.csv(dfo, file, row.names=FALSE) write.csv(dfo, file, row.names=FALSE)
...@@ -1047,7 +1051,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos ...@@ -1047,7 +1051,7 @@ The Heatmap is exportable in .png.", title=strong("Heatmap page Help"), easyClos
}) })
} }
### ----------------------------- Run the app ----------------------------------------------------- ### ----------------------------- Run the app -----------------------------------------------------
shinyApp(ui, server) shinyApp(ui, server)
www/chu.png

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www/crcina.png

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www/crcina.png
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