v1.2 cleanup

vibbits · Jun 1, 2022 · 864a33d · 864a33d
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diff --git a/Dockerfile b/Dockerfile
diff --git a/..._data/Input_meta_Escher-Trace_Example.zip → ..._data/Input_meta_Escher-Trace_Example.zip b/..._data/Input_meta_Escher-Trace_Example.zip → ..._data/Input_meta_Escher-Trace_Example.zip
diff --git a/...mple_data/Input_meta_abund_FC_Example.zip → Example_data/Input_meta_abund_FC_Example.zip b/...mple_data/Input_meta_abund_FC_Example.zip → Example_data/Input_meta_abund_FC_Example.zip
diff --git a/...ple_data/Input_meta_abund_iso_Example.zip → ...ple_data/Input_meta_abund_iso_Example.zip b/...ple_data/Input_meta_abund_iso_Example.zip → ...ple_data/Input_meta_abund_iso_Example.zip
diff --git a/..._data/Original input/Input_Example_FC.csv → ..._data/Original input/Input_Example_FC.csv b/..._data/Original input/Input_Example_FC.csv → ..._data/Original input/Input_Example_FC.csv
diff --git a/... input/Input_Example_RA+isotopologues.csv → ... input/Input_Example_RA+isotopologues.csv b/... input/Input_Example_RA+isotopologues.csv → ... input/Input_Example_RA+isotopologues.csv
diff --git a/..._data/Original input/Input_Example_RA.csv → ..._data/Original input/Input_Example_RA.csv b/..._data/Original input/Input_Example_RA.csv → ..._data/Original input/Input_Example_RA.csv
diff --git a/...nal input/Input_Example_isotopologues.csv → ...nal input/Input_Example_isotopologues.csv b/...nal input/Input_Example_isotopologues.csv → ...nal input/Input_Example_isotopologues.csv
diff --git a/...Original input/Input_Example_metadata.csv → ...Original input/Input_Example_metadata.csv b/...Original input/Input_Example_metadata.csv → ...Original input/Input_Example_metadata.csv
diff --git a/..._Example_standardized w isotopologues.csv → ..._Example_standardized w isotopologues.csv b/..._Example_standardized w isotopologues.csv → ..._Example_standardized w isotopologues.csv
diff --git a/...ized input/Input_Example_standardized.csv → ...ized input/Input_Example_standardized.csv b/...ized input/Input_Example_standardized.csv → ...ized input/Input_Example_standardized.csv
diff --git a/...nctions and modules/TraVis_InputCleaner.R → Functions and modules/TraVis_InputCleaner.R b/...nctions and modules/TraVis_InputCleaner.R → Functions and modules/TraVis_InputCleaner.R
diff --git a/...tions and modules/TraVis_Pies_functions.R → ...tions and modules/TraVis_Pies_functions.R b/...tions and modules/TraVis_Pies_functions.R → ...tions and modules/TraVis_Pies_functions.R
diff --git a/...ctions and modules/TraVis_Visualisation.R → Functions and modules/TraVis_Visualisation.R b/...ctions and modules/TraVis_Visualisation.R → Functions and modules/TraVis_Visualisation.R
diff --git a/...Pies/Functions and modules/TraVis_input.R → Functions and modules/TraVis_input.R b/...Pies/Functions and modules/TraVis_input.R → Functions and modules/TraVis_input.R
diff --git a/...ies/Functions and modules/TraVis_output.R → Functions and modules/TraVis_output.R b/...ies/Functions and modules/TraVis_output.R → Functions and modules/TraVis_output.R
diff --git a/...ooting modules/TraVis_output_testmodule.R → ...ooting modules/TraVis_output_testmodule.R b/...ooting modules/TraVis_output_testmodule.R → ...ooting modules/TraVis_output_testmodule.R
@@ -1,149 +1,149 @@
-# Description ---------------------------------------------------
-
-###Author: Sam De Craemer
-#Vlaams Instituut voor Biotechnologie (VIB) and KULeuven
-#Metabolomics Expertise Center (MEC)
-
-###Summary: Travis Pies shiny module that takes in desired settings for pie
-# chart plots and applies them on a provided curated dataset to 
-# generate figures with them.
-
-###Input
-# desired settings for pie chart plots and Travis curated tibble
-
-###Output
-# figures saved locally to provided folder
-
-# Functions and libraries ---------------------------------------------------------------
-
-#libraries for UI
-library(shiny)
-library(shinyFeedback)   #for error messages on box
-library(shinyjs)      #for disable button
-library(shinyFiles)   #for saving locally
-
-#library for calling helper functions from r script
-library(here)    #to make r source from file location instead of magic stuff
-source(here::here("Functions and modules/TraVis_Pies_functions_beta.R"))
-
-
-
-
-#Shiny Modules-------------------------------------------------------------------
-travis_output_ui <- function(id) {
-  fluidPage(
-    #load shiny package elements
-
-    #Button to start process
-    fluidRow(
-      column(2,
-             actionButton(NS(id, "save_plots"),
-                                   label = "Save plots to directory")
-      )
-    )
-  )
-}
-
-travis_output_server <- function(id,v_settings,tb) {
-  moduleServer(id,function(input, output, session) {
-
-    #Write text to put on top as explanation, need to use server output to be able 
-    #to write multiple lines
-    output$text <- renderText({
-      paste0("<b>Test action button sheninigans.</b><br/><br/>")
-
-    })
-
-
-
-    ## do the action
-    observeEvent(input$save_plots,{
-    print(Sys.time())
-    })
-  })
-}
-
-#Wrap modules in caller function to test-------------------------------------------------------------------
-#to make correspond to input
-example_tb<-tibble(Sample = c("S1","S2","S3","S4","S1","S2","S3","S4",
-                              "S1","S2","S3","S4"),
-                   Cohort=c("coh1","coh1","coh2","coh3",
-                            "coh1","coh1","coh2","coh3",
-                            "coh1","coh1","coh2","coh3"),
-                   Mugwort2=c("Mugw1","Mugw1","Mugw2","Mugw2",
-                              "Mugw1","Mugw1","Mugw2","Mugw2",
-                              "Mugw1","Mugw1","Mugw2","Mugw2"),
-                   datatype=c("Abund","Abund","Abund","Abund",
-                              "FracCont","FracCont","FracCont","FracCont",
-                              "NormAbund","NormAbund","NormAbund","NormAbund"),
-                   Result = c(40005,45858,7000000,5000000,
-                              .5,.453,.32,1,
-                              400005,458058,700000,500000),
-                   Result2 = c(40005,4585824,7552123,50000,
-                               .8,.75,.32,0.3,
-                               400005,45805824,755123,5000))
-norm<-T
-
-#example without normalized abundance
-# example_tb<-tibble(Sample = c("S1","S2","S3","S4","S1","S2","S3","S4",
-#                               "S1","S2","S3","S4"),
-#                    Cohort=c("coh1","coh1","coh2","coh3",
-#                             "coh1","coh1","coh2","coh3",
-#                             "coh1","coh1","coh2","coh3"),
-#                    Mugwort2=c("Mugw1","Mugw1","Mugw2","Mugw2",
-#                               "Mugw1","Mugw1","Mugw2","Mugw2",
-#                               "Mugw1","Mugw1","Mugw2","Mugw2"),
-#                    datatype=c("Abund","Abund","Abund","Abund",
-#                               "FracCont","FracCont","FracCont","FracCont",
-#                               "Abund","Abund","Abund","Abund"),
-#                    Result = c(40005,45858,7000000,5000000,
-#                               .5,.453,.32,1,
-#                               400005,458058,700000,500000),
-#                    Result2 = c(40005,4585824,7552123,50000,
-#                                .8,.75,.32,0.3,
-#                                400005,45805824,755123,5000))
-#norm<-F
-
-datatype_index<-which(colnames(example_tb)=="datatype")
-
-example_tb<-mutate(example_tb,Sample= as.character(Sample),
-                   across(2:(datatype_index-1), as.factor))
-factorder_input<-unique(as.character(pull(example_tb[,2])))
-example_tb[,2]<-fct_relevel(pull(example_tb[,2]),factorder_input)
-
-example_settings<-list(finish=F,fact_name = "Cohort",
-                       fact_order=factorder_input,norm = norm,
-                       label_decimals = 0,
-                       min_lab_dist = 0.42,
-                       percent_add = F,
-                       FC_position = "center",
-                       col_labeling = c("#bfbfbf","#ffd966"),
-                       circlelinetypes = c(1,1,1,1),
-                       circlelinecolor = "gray",
-                       maxcol_facet= 4,
-                       include_name = T,show_P=F,alpha=0.7,
-                       font="sans",otherfontsize = 16,
-                       legendtitlesize =16,
-                       cohortsize = 18,
-                       include_legend = T,
-                       show_P=T)
-
-
-travis_output_app<- function() {
-  ui <- fluidPage(
-    travis_output_ui("output")
-  )
-
-
-  server <- function(input, output, session) {
-    travis_output_server("output",v_settings = 
-                           do.call("reactiveValues",example_settings),
-                        tb = reactive(example_tb))
-  }
-
-  shinyApp(ui, server)  
-}
-
-travis_output_app()
-
-
+# Description ---------------------------------------------------
+
+###Author: Sam De Craemer
+#Vlaams Instituut voor Biotechnologie (VIB) and KULeuven
+#Metabolomics Expertise Center (MEC)
+
+###Summary: Travis Pies shiny module that takes in desired settings for pie
+# chart plots and applies them on a provided curated dataset to 
+# generate figures with them.
+
+###Input
+# desired settings for pie chart plots and Travis curated tibble
+
+###Output
+# figures saved locally to provided folder
+
+# Functions and libraries ---------------------------------------------------------------
+
+#libraries for UI
+library(shiny)
+library(shinyFeedback)   #for error messages on box
+library(shinyjs)      #for disable button
+library(shinyFiles)   #for saving locally
+
+#library for calling helper functions from r script
+library(here)    #to make r source from file location instead of magic stuff
+source(here::here("Functions and modules/TraVis_Pies_functions_beta.R"))
+
+
+
+
+#Shiny Modules-------------------------------------------------------------------
+travis_output_ui <- function(id) {
+  fluidPage(
+    #load shiny package elements
+
+    #Button to start process
+    fluidRow(
+      column(2,
+             actionButton(NS(id, "save_plots"),
+                                   label = "Save plots to directory")
+      )
+    )
+  )
+}
+
+travis_output_server <- function(id,v_settings,tb) {
+  moduleServer(id,function(input, output, session) {
+
+    #Write text to put on top as explanation, need to use server output to be able 
+    #to write multiple lines
+    output$text <- renderText({
+      paste0("<b>Test action button sheninigans.</b><br/><br/>")
+
+    })
+
+
+
+    ## do the action
+    observeEvent(input$save_plots,{
+    print(Sys.time())
+    })
+  })
+}
+
+#Wrap modules in caller function to test-------------------------------------------------------------------
+#to make correspond to input
+example_tb<-tibble(Sample = c("S1","S2","S3","S4","S1","S2","S3","S4",
+                              "S1","S2","S3","S4"),
+                   Cohort=c("coh1","coh1","coh2","coh3",
+                            "coh1","coh1","coh2","coh3",
+                            "coh1","coh1","coh2","coh3"),
+                   Mugwort2=c("Mugw1","Mugw1","Mugw2","Mugw2",
+                              "Mugw1","Mugw1","Mugw2","Mugw2",
+                              "Mugw1","Mugw1","Mugw2","Mugw2"),
+                   datatype=c("Abund","Abund","Abund","Abund",
+                              "FracCont","FracCont","FracCont","FracCont",
+                              "NormAbund","NormAbund","NormAbund","NormAbund"),
+                   Result = c(40005,45858,7000000,5000000,
+                              .5,.453,.32,1,
+                              400005,458058,700000,500000),
+                   Result2 = c(40005,4585824,7552123,50000,
+                               .8,.75,.32,0.3,
+                               400005,45805824,755123,5000))
+norm<-T
+
+#example without normalized abundance
+# example_tb<-tibble(Sample = c("S1","S2","S3","S4","S1","S2","S3","S4",
+#                               "S1","S2","S3","S4"),
+#                    Cohort=c("coh1","coh1","coh2","coh3",
+#                             "coh1","coh1","coh2","coh3",
+#                             "coh1","coh1","coh2","coh3"),
+#                    Mugwort2=c("Mugw1","Mugw1","Mugw2","Mugw2",
+#                               "Mugw1","Mugw1","Mugw2","Mugw2",
+#                               "Mugw1","Mugw1","Mugw2","Mugw2"),
+#                    datatype=c("Abund","Abund","Abund","Abund",
+#                               "FracCont","FracCont","FracCont","FracCont",
+#                               "Abund","Abund","Abund","Abund"),
+#                    Result = c(40005,45858,7000000,5000000,
+#                               .5,.453,.32,1,
+#                               400005,458058,700000,500000),
+#                    Result2 = c(40005,4585824,7552123,50000,
+#                                .8,.75,.32,0.3,
+#                                400005,45805824,755123,5000))
+#norm<-F
+
+datatype_index<-which(colnames(example_tb)=="datatype")
+
+example_tb<-mutate(example_tb,Sample= as.character(Sample),
+                   across(2:(datatype_index-1), as.factor))
+factorder_input<-unique(as.character(pull(example_tb[,2])))
+example_tb[,2]<-fct_relevel(pull(example_tb[,2]),factorder_input)
+
+example_settings<-list(finish=F,fact_name = "Cohort",
+                       fact_order=factorder_input,norm = norm,
+                       label_decimals = 0,
+                       min_lab_dist = 0.42,
+                       percent_add = F,
+                       FC_position = "center",
+                       col_labeling = c("#bfbfbf","#ffd966"),
+                       circlelinetypes = c(1,1,1,1),
+                       circlelinecolor = "gray",
+                       maxcol_facet= 4,
+                       include_name = T,show_P=F,alpha=0.7,
+                       font="sans",otherfontsize = 16,
+                       legendtitlesize =16,
+                       cohortsize = 18,
+                       include_legend = T,
+                       show_P=T)
+
+
+travis_output_app<- function() {
+  ui <- fluidPage(
+    travis_output_ui("output")
+  )
+
+
+  server <- function(input, output, session) {
+    travis_output_server("output",v_settings = 
+                           do.call("reactiveValues",example_settings),
+                        tb = reactive(example_tb))
+  }
+
+  shinyApp(ui, server)  
+}
+
+travis_output_app()
+
+