marcelcosta/invivos
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Correct 'cuttofs'

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marcelcosta
2020-11-13 20:03:51 +01:00
parent 1e051abf75
commit bac2a29200
1 changed files with 5 additions and 8 deletions
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invivos/app.R
+4 -7
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@@ -244,7 +244,6 @@ server <- function(input, output) {
observeEvent(analysis$taula, {}) observeEvent(analysis$taula, {})
stattest<-"dunn" stattest<-"dunn"
oneside<-"" oneside<-""
cutoff<-750
table<-analysis$taula table<-analysis$taula
if ("ID.animal" %in% colnames(table)){table<-rename(table, "ID animal"=`ID.animal`)} if ("ID.animal" %in% colnames(table)){table<-rename(table, "ID animal"=`ID.animal`)}
@@ -339,7 +338,7 @@ server <- function(input, output) {
g<-list() g<-list()
for (side in c("L","R")){ for (side in c("L","R")){
tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume)) tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume))
endtime<-dcast(tableR %>% filter(Volume < cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") endtime<-dcast(tableR %>% filter(Volume < input$cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
endtime["Dead"]<-dcast(tableR, Cage+`ID animal`+`ID tumor`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff endtime["Dead"]<-dcast(tableR, Cage+`ID animal`+`ID tumor`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
table_tumor<<-endtime table_tumor<<-endtime
@@ -363,7 +362,7 @@ server <- function(input, output) {
}else{ }else{
tableR<-table %>% filter(!is.na(Volume)) tableR<-table %>% filter(!is.na(Volume))
endtime<-dcast(tableR %>% filter(Volume < cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") endtime<-dcast(tableR %>% filter(Volume < input$cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
endtime["Dead"]<-dcast(tableR, `ID animal`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff endtime["Dead"]<-dcast(tableR, `ID animal`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
table_tumor<<-endtime table_tumor<<-endtime
@@ -381,7 +380,6 @@ server <- function(input, output) {
output$stats<-renderPrint({ output$stats<-renderPrint({
stattest<-"dunn" stattest<-"dunn"
oneside<-"" oneside<-""
cutoff<-750
if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){ if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
observeEvent(analysis$taula_def, {}) observeEvent(analysis$taula_def, {})
table<-analysis$taula_def table<-analysis$taula_def
@@ -403,7 +401,6 @@ server <- function(input, output) {
output$tab_stats<-renderTable({ output$tab_stats<-renderTable({
stattest<-"dunn" stattest<-"dunn"
oneside<-"" oneside<-""
cutoff<-750
if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){ if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
table<-analysis$taula_def table<-analysis$taula_def
table_stats<-list() table_stats<-list()
@@ -519,7 +516,7 @@ server <- function(input, output) {
count<-1 count<-1
for (side in c("L","R")){ for (side in c("L","R")){
tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume)) tableR<-filter(table, `ID tumor` == side) %>% filter(!is.na(Volume))
endtime<-dcast(tableR %>% filter(Volume < cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") endtime<-dcast(tableR %>% filter(Volume < input$cutoff), Cage+`ID animal`+`ID tumor`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
endtime["Dead"]<-dcast(tableR, Cage+`ID animal`+`ID tumor`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff endtime["Dead"]<-dcast(tableR, Cage+`ID animal`+`ID tumor`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
table_tumor<-endtime table_tumor<-endtime
if (input$colors != ""){ if (input$colors != ""){
@@ -540,7 +537,7 @@ server <- function(input, output) {
}else{ }else{
tableR<-table %>% filter(!is.na(Volume)) tableR<-table %>% filter(!is.na(Volume))
endtime<-dcast(tableR %>% filter(Volume < cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") endtime<-dcast(tableR %>% filter(Volume < input$cutoff), `ID animal`+Group~., value.var = "Timepoint", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
endtime["Dead"]<-dcast(tableR, `ID animal`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff endtime["Dead"]<-dcast(tableR, `ID animal`+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
table_tumor<-endtime table_tumor<-endtime
if (input$colors != ""){ if (input$colors != ""){