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Merge pull request #2 from JoachimGoedhart/Autofileformat
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Autofileformat
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@JoachimGoedhart
JoachimGoedhart authored May 26, 2020
2 parents 36e3ca4 + 94eefae commit 7ed197e
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119 changes: 71 additions & 48 deletions app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,8 @@ df_example_diffgenes_HFHC <- read.csv("Becares-diffgenes_HFHC.csv", na.strings =
# Create a reactive object here that we can share between all the sessions.
vals <- reactiveValues(count=0)



# Define UI
ui <- fluidPage(

Expand Down Expand Up @@ -241,30 +243,33 @@ ui <- fluidPage(
condition = "input.data_input=='3'",

fileInput("upload", NULL, multiple = FALSE, accept = c(".xlsx", ".xls", ".txt", ".csv")),
selectInput("file_type", "Type of file:",
list(".csv or .txt" = "text",
".xls or .xlsx" = "excel"
),
selected = "text"),
conditionalPanel(
condition = "input.file_type!='excel'",
radioButtons(
"upload_delim", "Delimiter",
choices =
list("Comma" = ",",
"Tab" = "\t",
"Semicolon" = ";",
"Space" = " ")),
selected = ","),
# selectInput("file_type", "Type of file:",
# list(".csv or .txt" = "text",
# ".xls or .xlsx" = "excel"
# ),
# selected = "text"),

# radioButtons(
# "upload_delim", "Delimiter",
# choices =
# list("Comma" = ",",
# "Tab" = "\t",
# "Semicolon" = ";",
# "Space" = " ")),
# selected = ","),

selectInput("upload_delim", label = "Select Delimiter (for text file):", choices =list("Comma" = ",",
"Tab" = "\t",
"Semicolon" = ";",
"Space" = " ")),

conditionalPanel(
condition = "input.file_type=='excel'",
selectInput("sheet", label = "Select sheet:", choices = " ")

),
selectInput("sheet", label = "Select sheet (for excel workbook):", choices = " ")




actionButton("submit_datafile_button", "Submit datafile")
# actionButton("submit_datafile_button", "Submit datafile")

),
### csv via URL as input
Expand Down Expand Up @@ -390,7 +395,7 @@ df_upload <- reactive({
if (input$data_input == 1) {
x_var.selected <<- "log2_FoldChange"
y_var.selected <<- "minus_log10_pvalue"
gene.selected <<- "Gene"
g_var.selected <<- "Gene"
genelist.selected <<- ""
# updateCheckboxInput(session, "transformation", value = FALSE)
# transform_var_x.selected <<- "-"
Expand All @@ -400,7 +405,7 @@ df_upload <- reactive({
} else if (input$data_input == 2) {
x_var.selected <<- "log2_FoldChange"
y_var.selected <<- "minus_log10_pvalue"
gene.selected <<- "Gene"
g_var.selected <<- "Gene"
genelist.selected <<- "HSPA6"
# updateCheckboxInput(session, "transformation", value = FALSE)
# transform_var_x.selected <<- "-"
Expand All @@ -415,16 +420,25 @@ df_upload <- reactive({
file_in <- input$upload
# Avoid error message while file is not uploaded yet
if (is.null(input$upload)) {
return(data.frame(x = "Select your datafile"))
} else if (input$submit_datafile_button == 0) {
return(data.frame(x = "Press 'submit datafile' button"))
return(data.frame(x = "Click 'Browse...' to select a datafile or drop file onto 'Browse' button"))
# } else if (input$submit_datafile_button == 0) {
# return(data.frame(x = "Press 'submit datafile' button"))
} else {
isolate({

#Isolate extenstion and convert to lowercase
filename_split <- strsplit(file_in$datapath, '[.]')[[1]]
fileext <- tolower(filename_split[length(filename_split)])

# observe({print(fileext)})

# isolate({
# data <- read.csv(file=file_in$datapath, sep = input$upload_delim, na.strings=c("",".","NA", "NaN", "#N/A", "#VALUE!"))

if (input$file_type == "text") {
if (fileext == "txt" || fileext=="csv") {

data <- read.csv(file=file_in$datapath, sep = input$upload_delim, na.strings=c("",".","NA", "NaN", "#N/A", "#VALUE!"))
} else if (input$file_type == "excel") {
updateSelectInput(session, "sheet", choices = " ", selected = " ")
} else if (fileext=="xls" || fileext=="xlsx") {
names <- excel_sheets(path = input$upload$datapath)
# updateSelectInput(session, "sheet_names", choices = names)
sheet.selected <<- input$sheet
Expand All @@ -445,11 +459,11 @@ df_upload <- reactive({
data <- read_excel(file_in$datapath, sheet = n , na = c("",".","NA", "NaN", "#N/A", "#VALUE!"))
}

})
# })
}

} else if (input$data_input == 5) {
genelist.selected <<- ""
# genelist.selected <<- ""
# updateCheckboxInput(session, "transformation", value = FALSE)
# transform_var_x.selected <<- "-"
# transform_var_y.selected <<- "-"
Expand Down Expand Up @@ -606,7 +620,6 @@ observe({

presets_can <- query[['can']]
presets_can <- unlist(strsplit(presets_can,";"))
observe(print((presets_can)))

updateNumericInput(session, "top_x", value = presets_can[1])
updateCheckboxInput(session, "show_table", value = presets_can[2])
Expand All @@ -615,6 +628,7 @@ observe({
# updateTextInput(session, "user_gene_list", value= presets_can[4])

genelist.selected <<- unlist(strsplit(presets_can[4],","))
# observe({print(genelist.selected)})

}

Expand Down Expand Up @@ -720,6 +734,7 @@ url <- reactive({
#Convert the list of genes to a comma-seperated string
a <- input$user_gene_list
a <- paste(a, collapse=",")
# observe({print(a)})

#as.character is necessary; if omitted TRUE is converted to 0 and FALSE to 1 which is undesired
can <- c(input$top_x, as.character(input$show_table), input$hide_labels, a)
Expand Down Expand Up @@ -817,17 +832,17 @@ observeEvent(input$settings_copy , {


if (input$criterion == "manh") {
df <- df %>% mutate(`Manhattan distance` = abs(`Significance`)+abs(`Fold change`)) %>% arrange(desc(`Manhattan distance`))
df_out <- df %>% top_n(input$top_x,`Manhattan distance`) %>% select(Name, Change, `Fold change`,`Significance`,`Manhattan distance`)
df <- df %>% mutate(`Manhattan distance` = abs(`Significance`)+abs(`Fold change (log2)`)) %>% arrange(desc(`Manhattan distance`))
df_out <- df %>% top_n(input$top_x,`Manhattan distance`) %>% select(Name, Change, `Fold change (log2)`,`Significance`,`Manhattan distance`)
} else if (input$criterion == "euclid") {
df <- df %>% mutate(`Euclidean distance` = sqrt((`Significance`)^2+(`Fold change`)^2)) %>% arrange(desc(`Euclidean distance`))
df_out <- df %>% top_n(input$top_x,`Euclidean distance`) %>% select(Name, Change, `Fold change`,`Significance`,`Euclidean distance`)
df <- df %>% mutate(`Euclidean distance` = sqrt((`Significance`)^2+(`Fold change (log2)`)^2)) %>% arrange(desc(`Euclidean distance`))
df_out <- df %>% top_n(input$top_x,`Euclidean distance`) %>% select(Name, Change, `Fold change (log2)`,`Significance`,`Euclidean distance`)
} else if (input$criterion == "fc") {
df <- df %>% arrange(desc(abs(`Fold change`)))
df_out <- df %>% top_n(input$top_x,abs(`Fold change`)) %>% select(Name, Change, `Fold change`,`Significance`)
df <- df %>% arrange(desc(abs(`Fold change (log2)`)))
df_out <- df %>% top_n(input$top_x,abs(`Fold change (log2)`)) %>% select(Name, Change, `Fold change (log2)`,`Significance`)
} else if (input$criterion == "sig") {
df <- df %>% arrange(desc(`Significance`))
df_out <- df %>% top_n(input$top_x,`Significance`) %>% select(Name, Change, `Fold change`,`Significance`)
df_out <- df %>% top_n(input$top_x,`Significance`) %>% select(Name, Change, `Fold change (log2)`,`Significance`)
}

#Add user selected hits, but remove them when already present
Expand Down Expand Up @@ -902,10 +917,10 @@ df_filtered <- reactive({


if (g_choice == "-") {
koos <- df %>% select(`Fold change` = !!x_choice , `Significance` = !!y_choice)
koos <- df %>% select(`Fold change (log2)` = !!x_choice , `Significance` = !!y_choice)
koos$Name <- " "
} else if (g_choice != "-") {
koos <- df %>% select(`Fold change` = !!x_choice , `Significance` = !!y_choice, Name = input$g_var)
koos <- df %>% select(`Fold change (log2)` = !!x_choice , `Significance` = !!y_choice, Name = input$g_var)
#Remove names after semicolon for hits with multiple names, seperated by semicolons, e.g.: POLR2J3;POLR2J;POLR2J2
koos <- koos %>% mutate(Name = gsub(';.*','',Name))

Expand All @@ -925,20 +940,20 @@ df_filtered <- reactive({
if (input$direction =="decreased") {
koos <- koos %>%mutate(
Change = case_when(
`Fold change` < foldchange_min & `Significance` > pvalue_tr ~ "Decreased",
`Fold change (log2)` < foldchange_min & `Significance` > pvalue_tr ~ "Decreased",
TRUE ~ "Unchanged")
)
} else if (input$direction =="increased") {
koos <- koos %>%mutate(
Change = case_when(
`Fold change` > foldchange_max & `Significance` > pvalue_tr ~ "Increased",
`Fold change (log2)` > foldchange_max & `Significance` > pvalue_tr ~ "Increased",
TRUE ~ "Unchanged")
)
} else {
koos <- koos %>%mutate(
Change = case_when(
`Fold change` > foldchange_max & `Significance` > pvalue_tr ~ "Increased",
`Fold change` < foldchange_min & `Significance` > pvalue_tr ~ "Decreased",
`Fold change (log2)` > foldchange_max & `Significance` > pvalue_tr ~ "Increased",
`Fold change (log2)` < foldchange_min & `Significance` > pvalue_tr ~ "Decreased",
TRUE ~ "Unchanged")
)
}
Expand Down Expand Up @@ -988,7 +1003,7 @@ plot_data <- reactive({
df$Change <- factor(df$Change, levels=c("Unchanged","Increased","Decreased"))

p <- ggplot(data = df) +
aes(x=`Fold change`) +
aes(x=`Fold change (log2)`) +
aes(y=`Significance`) +
geom_point(alpha = input$alphaInput, size = input$pointSize, shape = 16) +

Expand All @@ -1014,7 +1029,7 @@ plot_data <- reactive({

########## User defined labeling
if (input$hide_labels == FALSE) {
p <- p + geom_point(data=df_top(), aes(x=`Fold change`,y=`Significance`), shape=1,color="black", size=(input$pointSize))+
p <- p + geom_point(data=df_top(), aes(x=`Fold change (log2)`,y=`Significance`), shape=1,color="black", size=(input$pointSize))+
geom_text_repel(
data = df_top(),
aes(label = Name),
Expand Down Expand Up @@ -1056,6 +1071,10 @@ plot_data <- reactive({
#Add line break to generate some space
title <- paste(input$title, "\n",sep="")
p <- p + labs(title = title)
} else if (input$sheet !=" ") {
title <- paste(input$sheet, "\n",sep="")
# observe({print('yay')})
p <- p + labs(title = title)
}

# # if labels specified
Expand Down Expand Up @@ -1152,7 +1171,7 @@ output$coolplot <- renderPlot(width = width, height = height,{


p <- ggplot(data = df) +
aes(x=`Fold change`) +
aes(x=`Fold change (log2)`) +
aes(y=`Significance`) +
geom_point(alpha = input$alphaInput, size = input$pointSize, shape = 16) +

Expand Down Expand Up @@ -1180,7 +1199,7 @@ output$coolplot <- renderPlot(width = width, height = height,{

########## User defined labeling
if (input$hide_labels == FALSE) {
p <- p + geom_point(data=df_top(), aes(x=`Fold change`,y=`Significance`), shape=1,color="black", size=(input$pointSize))+
p <- p + geom_point(data=df_top(), aes(x=`Fold change (log2)`,y=`Significance`), shape=1,color="black", size=(input$pointSize))+
geom_text_repel(
data = df_top(),
aes(label = Name),
Expand Down Expand Up @@ -1221,6 +1240,10 @@ output$coolplot <- renderPlot(width = width, height = height,{
#Add line break to generate some space
title <- paste(input$title, "\n",sep="")
p <- p + labs(title = title)
} else if (input$sheet !=" ") {
title <- paste(input$sheet, "\n",sep="")
# observe({print('yay')})
p <- p + labs(title = title)
}

# # if labels specified
Expand Down
4 changes: 2 additions & 2 deletions rsconnect/shinyapps.io/goedhart/VolcaNoseR.dcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,9 @@ account: goedhart
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 1844600
bundleId: 3152936
bundleId: 3187585
url: https://goedhart.shinyapps.io/VolcaNoseR/
when: 1589568277.55335
when: 1590415810.85185
asMultiple: FALSE
asStatic: FALSE
ignoredFiles: .gitattributes|LICENSE|README.md|VolcaNoseR_example1.png|VolcaNoseR_example2.png

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