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marcelcosta/invivos:master

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fd6493320f ... 9f0cda73eb

Author SHA1 Message Date
marcelcosta 9f0cda73eb Corrección del Survival y implementación de corte de operados y eliminación de muertes. 2023-10-05 17:30:36 +02:00
marcelcosta 16088aac2b Implementar la posibilidad de eliminar los ratones que hayan muerto prematuramente. 2023-10-05 17:23:39 +02:00
1 changed files with 143 additions and 5 deletions
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invivos/app.R
+143 -5
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@@ -48,6 +48,7 @@ ui <- fluidPage(
checkboxInput("filter_stats","Filtrar Estadística"), checkboxInput("filter_stats","Filtrar Estadística"),
checkboxInput("increase_volume","Usar Incremento de Volumen"), checkboxInput("increase_volume","Usar Incremento de Volumen"),
checkboxInput("operated","Cortar al operar", value = TRUE), checkboxInput("operated","Cortar al operar", value = TRUE),
checkboxInput("dead","Eliminar ratones muertos", value = FALSE),
downloadButton("downloadVolume", "Descargar Volúmenes") downloadButton("downloadVolume", "Descargar Volúmenes")
), ),
mainPanel( mainPanel(
@@ -456,11 +457,17 @@ server <- function(input, output) {
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>% firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
select(DayPostInoc, Side) %>% unique() %>% select(DayPostInoc, Side) %>% unique() %>%
group_by(Side) %>% summarise(FirstOper=min(DayPostInoc)) group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
print(deadmice)
if (input$operated == TRUE){ if (input$operated == TRUE){
for (i in 1:nrow(firstoper)){ for (i in 1:nrow(firstoper)){
table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i]) table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
} }
}else{
if(input$dead == TRUE){
table<-table %>% filter(!Animal %in% deadmice)
}
} }
ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+ ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+
@@ -480,6 +487,12 @@ server <- function(input, output) {
if (input$operated == TRUE){ if (input$operated == TRUE){
table<-table %>% filter(DayPostInoc < firstoper) table<-table %>% filter(DayPostInoc < firstoper)
}else{
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
if(input$dead == TRUE){
table<-table %>% filter(!Animal %in% deadmice)
}
} }
ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+ ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Group))+
@@ -518,6 +531,20 @@ server <- function(input, output) {
table<-rbind(table, basal) table<-rbind(table, basal)
if (input$vacc == "Sí"){ if (input$vacc == "Sí"){
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
select(DayPostInoc, Side) %>% unique() %>%
group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
if (input$operated == TRUE){
for (i in 1:nrow(firstoper)){
table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
}
}else{
if(input$dead == TRUE){
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
table<-table %>% filter(!Animal %in% deadmice)
}
}
ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Animal))+ ggplot(table, aes(DayPostInoc, Volume, color=Group, group=Animal))+
# geom_errorbar(stat="summary", width=0.05)+ # geom_errorbar(stat="summary", width=0.05)+
geom_line()+ geom_line()+
@@ -528,6 +555,19 @@ server <- function(input, output) {
labs(x="Days after tumor inoculation")+ labs(x="Days after tumor inoculation")+
theme_bw() theme_bw()
}else{ }else{
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
pull(DayPostInoc) %>% min(na.rm = T)
print(firstoper)
if (input$operated == TRUE){
table<-table %>% filter(DayPostInoc < firstoper)
}else{
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
if(input$dead == TRUE){
table<-table %>% filter(!Animal %in% deadmice)
}
}
ggplot(table, aes(DayPostInoc, Volume, color=Group, group=paste0(Animal, Side)))+ ggplot(table, aes(DayPostInoc, Volume, color=Group, group=paste0(Animal, Side)))+
# geom_errorbar(stat="summary", width=0.05)+ # geom_errorbar(stat="summary", width=0.05)+
geom_line()+ geom_line()+
@@ -547,6 +587,20 @@ server <- function(input, output) {
observeEvent(analysis$taula, {}) observeEvent(analysis$taula, {})
table<-analysis$taula table<-analysis$taula
if (input$vacc == "Sí"){ if (input$vacc == "Sí"){
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
select(DayPostInoc, Side) %>% unique() %>%
group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
if (input$operated == TRUE){
for (i in 1:nrow(firstoper)){
table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
}
}else{
if(input$dead == TRUE){
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
table<-table %>% filter(!Animal %in% deadmice)
}
}
g<-list() g<-list()
for (side in c("L","R")){ for (side in c("L","R")){
tableR<-filter(table, Side == side) %>% filter(!is.na(Volume)) tableR<-filter(table, Side == side) %>% filter(!is.na(Volume))
@@ -554,7 +608,7 @@ server <- function(input, output) {
endtime["Dead"]<-dcast(tableR, Cage+Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff endtime["Dead"]<-dcast(tableR, Cage+Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > input$cutoff
table_tumor<<-endtime table_tumor<<-endtime
g[side]<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor), g[side]<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor),
pval = T, pval.method = T, pval = T, pval.method = T,
title = side, title = side,
# legend.labs = paste(c("< median", ">= median"), "MICA"), # legend.labs = paste(c("< median", ">= median"), "MICA"),
@@ -573,13 +627,27 @@ server <- function(input, output) {
do.call(grid.arrange, g) do.call(grid.arrange, g)
}else{ }else{
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
pull(DayPostInoc) %>% min(na.rm = T)
print(firstoper)
if (input$operated == TRUE){
table<-table %>% filter(DayPostInoc < firstoper)
}else{
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
if(input$dead == TRUE){
table<-table %>% filter(!Animal %in% deadmice)
}
}
tableR<-table %>% filter(!is.na(Volume)) tableR<-table %>% filter(!is.na(Volume))
endtime<-dcast(if(length(unique(tableR$DayPostInoc)) > 1){tableR %>% filter(Volume < input$cutoff)}else{tableR}, Animal+Side+Group~., endtime<-dcast(if(length(unique(tableR$DayPostInoc)) > 1){tableR %>% filter(Volume < input$cutoff)}else{tableR}, Animal+Side+Group~.,
value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
endtime["Dead"]<-dcast(tableR, Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") >= input$cutoff endtime["Dead"]<-dcast(tableR, Animal+Side+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") >= input$cutoff
table_tumor<<-endtime table_tumor<<-endtime
g<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ table_tumor$Group, data=table_tumor), g<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor),
pval = T, pval.method = T, pval = T, pval.method = T,
# legend.labs = paste(c("< median", ">= median"), "MICA"), # legend.labs = paste(c("< median", ">= median"), "MICA"),
ggtheme=theme_classic(base_size=15) ggtheme=theme_classic(base_size=15)
@@ -713,6 +781,12 @@ server <- function(input, output) {
for (i in 1:nrow(firstoper)){ for (i in 1:nrow(firstoper)){
table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i]) table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
} }
}else{
if(input$dead == TRUE){
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
table<-table %>% filter(!Animal %in% deadmice)
}
} }
std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))} std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))}
errbar<-table %>% group_by(Group,Side,DayPostInoc) %>% errbar<-table %>% group_by(Group,Side,DayPostInoc) %>%
@@ -739,7 +813,14 @@ server <- function(input, output) {
if (input$operated == TRUE){ if (input$operated == TRUE){
table<-table %>% filter(DayPostInoc < firstoper) table<-table %>% filter(DayPostInoc < firstoper)
}else{
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
if(input$dead == TRUE){
table<-table %>% filter(!Animal %in% deadmice)
}
} }
std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))} std<-function(x, na.rm=T){sd(x, na.rm=na.rm)/sqrt(length(x))}
errbar<-table %>% group_by(Group, DayPostInoc) %>% errbar<-table %>% group_by(Group, DayPostInoc) %>%
summarise(mean=mean(Volume, na.rm=T), std=std(Volume)) %>% summarise(mean=mean(Volume, na.rm=T), std=std(Volume)) %>%
@@ -761,6 +842,22 @@ server <- function(input, output) {
} }
if (input$fig_id == "Cinética Individual"){ if (input$fig_id == "Cinética Individual"){
if (input$vacc == "Sí"){ if (input$vacc == "Sí"){
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
select(DayPostInoc, Side) %>% unique() %>%
group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
if (input$operated == TRUE){
for (i in 1:nrow(firstoper)){
table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
}
}else{
if(input$dead == TRUE){
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
table<-table %>% filter(!Animal %in% deadmice)
}
}
g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+ g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+
scale_x_continuous(expand = expansion(mult = c(0,0.0)), scale_x_continuous(expand = expansion(mult = c(0,0.0)),
breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))), breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))),
@@ -768,6 +865,20 @@ server <- function(input, output) {
facet_grid(factor(Side, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+ facet_grid(factor(Side, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+
theme_bw() theme_bw()
}else{ }else{
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
pull(DayPostInoc) %>% min(na.rm = T)
print(firstoper)
if (input$operated == TRUE){
table<-table %>% filter(DayPostInoc < firstoper)
}else{
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
if(input$dead == TRUE){
table<-table %>% filter(!Animal %in% deadmice)
}
}
g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+ g<-ggplot(table, aes(as.numeric(as.character(DayPostInoc)), Volume, color=Group, group=Animal))+
scale_x_continuous(expand = expansion(mult = c(0,0.0)), scale_x_continuous(expand = expansion(mult = c(0,0.0)),
breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))), breaks=sort(unique(as.numeric(as.character(table$DayPostInoc)))),
@@ -818,6 +929,20 @@ server <- function(input, output) {
} }
if (input$vacc == "Sí"){ if (input$vacc == "Sí"){
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
select(DayPostInoc, Side) %>% unique() %>%
group_by(Side) %>% summarise(FirstOper=min(DayPostInoc))
if (input$operated == TRUE){
for (i in 1:nrow(firstoper)){
table<-table %>% filter(DayPostInoc < firstoper$FirstOper[i] | Side != firstoper$Side[i])
}
}else{
if(input$dead == TRUE){
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
table<-table %>% filter(!Animal %in% deadmice)
}
}
g<-list() g<-list()
count<-1 count<-1
for (side in c("L","R")){ for (side in c("L","R")){
@@ -831,7 +956,7 @@ server <- function(input, output) {
col<-gg_color_hue(length(unique(endtime$Group))) col<-gg_color_hue(length(unique(endtime$Group)))
} }
table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group)) table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group))
g[[count]]<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ Group, data=table_tumor), g[[count]]<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor),
pval = T, pval.method = T, pval = T, pval.method = T,
title = side, title = side,
ggtheme=theme_classic(base_size=input$`font-size`), ggtheme=theme_classic(base_size=input$`font-size`),
@@ -842,6 +967,19 @@ server <- function(input, output) {
g_surv_vacc<-g g_surv_vacc<-g
}else{ }else{
firstoper<- filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "*") %>%
pull(DayPostInoc) %>% min(na.rm = T)
print(firstoper)
if (input$operated == TRUE){
table<-table %>% filter(DayPostInoc < firstoper)
}else{
deadmice<-filter(table, !is.na(substr(Observations,1,1)) & substr(Observations,1,1) == "+") %>%
pull(Animal)
if(input$dead == TRUE){
table<-table %>% filter(!Animal %in% deadmice)
}
}
tableR<-table %>% filter(!is.na(Volume)) tableR<-table %>% filter(!is.na(Volume))
endtime<-dcast(tableR %>% filter(Volume < (input$cutoff*as.numeric(input$unit_fact))), Animal+Group~., value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".") endtime<-dcast(tableR %>% filter(Volume < (input$cutoff*as.numeric(input$unit_fact))), Animal+Group~., value.var = "DayPostInoc", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% rename("end"=".")
endtime["Dead"]<-dcast(tableR, Animal+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > (input$cutoff*as.numeric(input$unit_fact)) endtime["Dead"]<-dcast(tableR, Animal+Group~., value.var = "Volume", fun.aggregate = function(x){max(as.numeric(as.character(x)))}) %>% pull(".") > (input$cutoff*as.numeric(input$unit_fact))
@@ -852,7 +990,7 @@ server <- function(input, output) {
col<-gg_color_hue(length(unique(table_tumor$Group))) col<-gg_color_hue(length(unique(table_tumor$Group)))
} }
table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group)) table_tumor$Group<-factor(table_tumor$Group, levels = levels(analysis$taula$Group))
g<-ggsurvplot(survfit(Surv(table_tumor$end, table_tumor$Dead) ~ Group, data=table_tumor), g<-ggsurvplot(survfit(Surv(end, Dead) ~ Group, data=table_tumor),
pval = T, pval.method = T, pval = T, pval.method = T,
# ggtheme=theme_classic(base_size=input$`font-size`), # ggtheme=theme_classic(base_size=input$`font-size`),
palette = col palette = col