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fix_test_data #442

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merged 9 commits into from
Feb 5, 2025
Merged

fix_test_data #442

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b30f955
Fixed a wrong artifact in test data (compared with original data on g…
PaulJonasJost Jan 25, 2025
9132fa1
Removed the upload data button in visual inspection and merged with t…
PaulJonasJost Jan 25, 2025
1d2515d
bug fixed - was due to missing input if uploaded data can be used as …
LeaSeep Feb 3, 2025
5eacbba
rm print statements
LeaSeep Feb 3, 2025
147e4e1
formatted data tables nicer according to #432
LeaSeep Feb 3, 2025
f00d310
Merge branch 'develop' into fix_test_data
LeaSeep Feb 3, 2025
6a058f6
fix tables accounting for difference in manual tab and DEseq tab
LeaSeep Feb 5, 2025
e94acb4
make default names clearer
LeaSeep Feb 5, 2025
cbc8a5a
added not for missing icons upon download
LeaSeep Feb 5, 2025
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114 changes: 54 additions & 60 deletions program/shinyApp/server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -475,10 +475,6 @@ server <- function(input,output,session){
title = "Upload Visual Inspection",
helpText("If you have uploaded your data, you might want to visually check the tables to confirm the correct data format. If you notice irregualarities you will need to correct the input data - this cannot be done in cOmicsArt, See the help on how your data is expected."),
br(),
actionButton(
inputId = "DoVisualDataInspection",
label = "Upload data for visual inspection"
) %>% helper(type = "markdown", content = "DataSelection_UploadInspection"),
splitLayout(
style = "border: 1px solid silver:", cellWidths = c("70%", "30%"),
DT::dataTableOutput("DataMatrix_VI"),
Expand All @@ -503,41 +499,16 @@ server <- function(input,output,session){
size = "l", # large modal
class = "custom-modal" # custom class for this modal
))
})

observeEvent(input$usingVIdata,{
if(res_tmp[[session$token]]$passedVI){
uploaded_from("VI_data")
removeModal()
# take specification from file_input as only here VI applicable
par_tmp[[session$token]]['omic_type'] <<- input[[paste0("omic_type_file_input")]]
omic_type(input[[paste0("omic_type_file_input")]])
shinyjs::click("refresh1")
}else{
show_toast(
title = "Data did not passed visual inspection. Data is not used and needs adjustments before reuploading and usage within cOmicsArt!",
type = "error",
position = "top",
timerProgressBar = FALSE,
width = "100%"
)
}

})
observeEvent(input$CloseVI,{
removeModal()
})

observeEvent(input$DoVisualDataInspection,{
tryCatch({
if(isTruthy(input$data_preDone)){
output$DataMatrix_VI_Info <- renderText({
"Visual Inspection only for primary data, not for precompiled set possible!"
})
req(F)
}
if(!(isTruthy(input$data_matrix1) &
(isTruthy(input$data_sample_anno1)|isTruthy(input$metadataInput)) &
if(!(isTruthy(input$data_matrix1) &
(isTruthy(input$data_sample_anno1)|isTruthy(input$metadataInput)) &
isTruthy(input$data_row_anno1))){
output$OverallChecks <- renderText(
"<font color=\"#ab020a\"><b>The Upload has failed completely, or you haven't uploaded anything yet. Need to uploade all three matrices!</b></font>"
Expand All @@ -557,7 +528,7 @@ server <- function(input,output,session){
)
}
)

if(flag_csv == F){
tryCatch(
expr = {
Expand All @@ -581,7 +552,7 @@ server <- function(input,output,session){
expr = {
withCallingHandlers(
{
dim(Matrix) # to envoke an error if it is not present
dim(Matrix) # to envoke an error if it is not present
# (needed sometime as DT sometimes seem to handle errors internally and does not throw an error)
# not the cleanest but works
output$DataMatrix_VI <- DT::renderDataTable({
Expand Down Expand Up @@ -633,13 +604,13 @@ server <- function(input,output,session){
check4 <- tryCatch(ifelse(any(is.na(sample_table) == T),snippetNo,snippetYes),error = function(e) snippetNo)
check5 <- tryCatch(ifelse(any(is.na(annotation_rows) == T),snippetNo,snippetYes),error = function(e) snippetNo)
check6 <- tryCatch(ifelse(all(colnames(Matrix2) == colnames(Matrix)),snippetYes,snippetNo),error = function(e) snippetNo)

check7 <- tryCatch(ifelse(all(sapply(Matrix,is.numeric)),snippetYes,snippetNo),error = function(e) snippetNo)
if(grepl(snippetYes,check0) &
grepl(snippetYes,check1) &
grepl(snippetYes,check2) &
grepl(snippetYes,check3) &

if(grepl(snippetYes,check0) &
grepl(snippetYes,check1) &
grepl(snippetYes,check2) &
grepl(snippetYes,check3) &
grepl(snippetYes,check4) & # not crucial
# grepl(snippetYes,check5) & # not crucial
grepl(snippetYes,check6) &
Expand Down Expand Up @@ -694,12 +665,12 @@ server <- function(input,output,session){
annotation_rows$original_rownames <- as.character(rownames(Matrix))
idxTochange <- grepl(invalidStart_regex, rownames(Matrix))
rownames(Matrix)[idxTochange] <- paste0("entite_", rownames(Matrix)[idxTochange])

idxTochange_space <- grepl(space_regex, rownames(Matrix))
rownames(Matrix)[idxTochange_space] <- gsub(space_regex,".",rownames(Matrix)[idxTochange_space])

allIdx_changes <- sort(unique(c(idxTochange_space,idxTochange)))

oldnames_matrix <- rownames(Matrix)[allIdx_changes]
newName_matrix <- rownames(Matrix)[allIdx_changes]
info_snippet_matrix_row <- paste0("Changes: <br> Matrix: Number of rownames changed: ",length(oldnames_matrix),"<br>",
Expand All @@ -716,12 +687,12 @@ server <- function(input,output,session){
colnames(Matrix) <- gsub("^X","",colnames(Matrix))
}
colnames(Matrix)[idxTochange] <- paste0("sample_", colnames(Matrix)[idxTochange])

idxTochange_space <- grepl(space_regex, colnames(Matrix))
colnames(Matrix)[idxTochange_space] <- gsub(space_regex,".",colnames(Matrix)[idxTochange_space])

allIdx_changes <- sort(unique(c(idxTochange_space,idxTochange)))

oldnames_matrix <- colnames(Matrix)[allIdx_changes]
newName_matrix <- colnames(Matrix)[allIdx_changes]
info_snippet_matrix_column <- paste0("Changes: <br> Matrix: Number of colnames changed: ",length(oldnames_matrix),"<br>",
Expand All @@ -733,12 +704,12 @@ server <- function(input,output,session){
if(any(grepl(invalidStart_regex, rownames(sample_table))) | any(grepl(space_regex, rownames(sample_table)))){
idxTochange <- grepl(invalidStart_regex, rownames(sample_table))
rownames(sample_table)[idxTochange] <- paste0("sample_", rownames(sample_table)[idxTochange])

idxTochange_space <- grepl(space_regex, rownames(sample_table))
rownames(sample_table)[idxTochange_space] <- gsub(space_regex,".",rownames(sample_table)[idxTochange_space])

allIdx_changes <- sort(unique(c(idxTochange_space,idxTochange)))

oldnames_sample <- rownames(sample_table)[allIdx_changes]
newName_sample <- rownames(sample_table)[allIdx_changes]
info_snippet_sample <- paste0("Changes: <br> Sample Table: Number of rownames changed: ",length(oldnames_sample),"<br>",
Expand All @@ -750,12 +721,12 @@ server <- function(input,output,session){
if(any(grepl(invalidStart_regex, rownames(annotation_rows))) | any(grepl(space_regex, rownames(annotation_rows)))){
idxTochange <- grepl(invalidStart_regex, rownames(annotation_rows))
rownames(annotation_rows)[idxTochange] <- paste0("entite_", rownames(annotation_rows)[idxTochange])

idxTochange_space <- grepl(space_regex, rownames(annotation_rows))
rownames(annotation_rows)[idxTochange_space] <- gsub(space_regex,".",rownames(annotation_rows)[idxTochange_space])

allIdx_changes <- sort(unique(c(idxTochange_space,idxTochange)))

oldnames_entitie <- rownames(annotation_rows)[allIdx_changes]
newNames_entitie <- rownames(annotation_rows)[allIdx_changes]
info_snippet_entitie <- paste0("Changes: <br> Entitie Table: Number of rownames changed: ",length(oldnames_entitie),"<br>",
Expand All @@ -764,16 +735,16 @@ server <- function(input,output,session){
}else{
info_snippet_entitie <- ""
}

# TODO if rownames updated put also to report

# Write the matrices to csv's to allow reupload for later
write.csv(Matrix, file = paste0("www/",session$token,"/updatedMatrix.csv"), row.names = T)
write.csv(sample_table, file = paste0("www/",session$token,"/updatedSampleTable.csv"), row.names = T)
write.csv(annotation_rows, file = paste0("www/",session$token,"/updatedEntitieAnnotation.csv"), row.names = T)

# TODO also set flag to update matrixes upon 'upload new data' within app for this round

showModal(modalDialog(
title = "Download Updated Data",
HTML(paste0("You can download your updated data for later reupload.<br>",
Expand Down Expand Up @@ -853,10 +824,10 @@ server <- function(input,output,session){
"Sample IDs have valid names ", check6, "\n"
)
})
if(grepl(snippetYes,check0) &
grepl(snippetYes,check1) &
grepl(snippetYes,check2) &
grepl(snippetYes,check3) &
if(grepl(snippetYes,check0) &
grepl(snippetYes,check1) &
grepl(snippetYes,check2) &
grepl(snippetYes,check3) &
grepl(snippetYes,check4) & # not crucial
# grepl(snippetYes,check5) & # not crucial
grepl(snippetYes,check6) &
Expand All @@ -865,10 +836,10 @@ server <- function(input,output,session){
} else {
res_tmp[[session$token]]$passedVI <<- F
}

})


})

if(check6 == "No"){
Expand Down Expand Up @@ -919,6 +890,29 @@ server <- function(input,output,session){
})
})

observeEvent(input$usingVIdata,{
if(res_tmp[[session$token]]$passedVI){
uploaded_from("VI_data")
removeModal()
# take specification from file_input as only here VI applicable
par_tmp[[session$token]]['omic_type'] <<- input[[paste0("omic_type_file_input")]]
omic_type(input[[paste0("omic_type_file_input")]])
shinyjs::click("refresh1")
}else{
show_toast(
title = "Data did not passed visual inspection. Data is not used and needs adjustments before reuploading and usage within cOmicsArt!",
type = "error",
position = "top",
timerProgressBar = FALSE,
width = "100%"
)
}

})
observeEvent(input$CloseVI,{
removeModal()
})


observeEvent(input$refresh_file_input, {
uploaded_from("file_input")
Expand Down
2 changes: 1 addition & 1 deletion program/shinyApp/www/airway-read-counts-LS.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@
"ENSG00000006530","303","276","344","203","420","467","268","277"
"ENSG00000006534"," 875","1108","1391"," 856","1521","2571"," 525"," 843"
"ENSG00000006576"," 924"," 653","1538"," 678","1347","1144","1454","1016"
"ENSG00000006606"," 3"," 4",NA," 1"," 7","10"," 2"," 2"
"ENSG00000006606"," 3"," 4"," 2"," 1"," 7","10"," 2"," 2"
"ENSG00000006607"," 652"," 733"," 924"," 776"," 674","1458"," 738","1144"
"ENSG00000006625","207","186","216","101","289","333","171","133"
"ENSG00000006634"," 98"," 70","104"," 48","113","103"," 96"," 72"
Expand Down
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