Pca worflow integrated #146
Conversation
…is" or add an info pop up?
# Conflicts: # program/shinyApp/ui.R
| @@ -16,7 +15,7 @@ source("R/enrichment_analysis/translation.R", local = T) | |||
| source("R/enrichment_analysis/server.R", local = T) | |||
| source("R/heatmap/server.R",local = T) | |||
| source("R/pca/server.R", local = T) | |||
| source("R/volcano_plot/server.R", local = T) | |||
| source("R/pca/util.R", local = T) | |||
There was a problem hiding this comment.
Do we want to name it utils.Rto be consistent with all utils files?
| adjustMethod | ||
| adjustMethod, | ||
| comp_type, | ||
| ref, |
There was a problem hiding this comment.
maybe renaming to `ctrl' - to be more clear
| input$sample_annotation_types_cmp_GSEA, | ||
| input$Groups2Compare_ref_GSEA, | ||
| input$Groups2Compare_treat_GSEA, | ||
| input$ValueToAttach |
There was a problem hiding this comment.
| input$ValueToAttach | |
| input$Value_to_attach |
| @@ -238,6 +237,9 @@ heatmap_server <- function(id, data, params, updates){ | |||
| input$PreProcessing_Procedure | |||
| ) | |||
|
|
|||
| ### atm raw data plotted | |||
There was a problem hiding this comment.
Is this a todo? Shouldn't the processed data be always used further?
| print(input$row_anno_options_heatmap) | ||
| additionalInput_row_anno <- ifelse(any(input$row_selection_options == "rowAnno_based"),"yip",NA) | ||
| if(!is.na(additionalInput_row_anno)){ | ||
| additionalInput_row_anno <- input$anno_options_heatmap | ||
| print(additionalInput_row_anno) | ||
| } | ||
| additionalInput_row_anno_factor <- input$row_anno_options_heatmap | ||
| #} # check if this is working if yes delete lines | ||
| #} # check if this is working if yes delete lines # @leaseep, is this checked |
There was a problem hiding this comment.
No, and I honestly do not remember what the issues was here.. Do you know? (As you just worked through this code base?)
There was a problem hiding this comment.
no, could not find anything specific.
| # workaround, as somehow the input values dont show up unless we change it in the shiny | ||
| # TODO: fix this (@Lea?) |
There was a problem hiding this comment.
I may misunderstand, but one reason could be that we only get the value of an reactive if it is actually called (or triggered due to change of that respective variable)
So to get the input values through 'toPlotVolcano' - reacive you need to wrap this in an 'observerEvent' or similiar
| @@ -39,6 +39,7 @@ library(kableExtra) | |||
| library(readxl) | |||
| library(ggvenn) | |||
| library(ComplexUpset) | |||
| library(gridExtra) # TODO: needs to be added to renv | |||
There was a problem hiding this comment.
should be available as a requirement for multiple other packages
|
Image somehow still broken but less important for now |
Co-authored-by: Lea Seep <[email protected]>
No description provided.