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invivos
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Adaptado la normalización a nuevo formato. Se puede indicar el día a normalizar.

master
marcelcosta 1 year ago
parent
0e4ef399fd
commit
35a73598d3
1 changed files with 64 additions and 63 deletions
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  1. +64
    -63
      invivos/app.R

+ 64
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invivos/app.R
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@ -26,6 +26,7 @@ ui <- fluidPage(
uiOutput('ncages'),
uiOutput('ntumors'),
# selectInput(inputId = "measure_sys", "Sistema de medida", selected = "L-W-D", choices = c("L-W-D","Min-Max","Absorbance")),
uiOutput('day_vol'),
uiOutput('lowcut'),
uiOutput('upcut'),
uiOutput('goButton'),
@ -103,22 +104,29 @@ server <- function(input, output) {
dades$db<-NULL
observe({
if (!is.null(input$file_sizes)){
taula<-read.xlsx(input$file_sizes$datapath, sheet = 1, sep.names = " ")
if ("DPV" %in% colnames(taula)){
taula<-dcast(taula, Cage+`ID animal`+`ID tumor`+Group~DPV, value.var = "0")
# taula$Major<-taula$Major/1000
# taula$Minor<-taula$Minor/1000
# taula["Volume"]<-((taula$Major*taula$Minor*taula$Minor)*(pi/6))*1000
taula$Major<-taula$Major
taula$Minor<-taula$Minor
taula["Volume"]<-((taula$Major*taula$Minor*taula$Minor)*(pi/6))
table<-read.xlsx(input$file_sizes$datapath, sheet = 1, check.names = F, sep.names = " ", detectDates = T,cols=1:11)
if("ID.animal" %in% colnames(table)){
table<-table %>%
rename(Animal=`ID.animal`, Side=`ID.tumor`)
table<-table %>% gather(DayPostInoc, Value, which(!is.na(as.numeric(colnames(table))))) %>%
relocate(DayPostInoc, .before = Group) %>% spread(DPV, Value) %>%
rename(Long=Major, Wide=Minor) %>%
add_column(Date="", .after = "Animal") %>%
add_column(Weight="", .after="Group") %>%
add_column(Volume="",Observations="") %>%
relocate(Side, .after = "Group")
table$DayPostInoc<-as.numeric(table$DayPostInoc)
}
if ("TS" %in% colnames(taula)){
taula<-dcast(taula, Cage+`ID animal`+`ID tumor`+Group~TS, value.var = "0")
taula["Volume"]<-taula$`TS-Deep`*taula$`TS-Length`*taula$`TS-Width`*pi/6
table$Date<-format(table$Date, format="%d/%m/%Y")
if ("sex" %in% colnames(table)){table<-select(table, -sex)}
for (i in 1:nrow(table)){
long<-as.numeric(gsub(",",".",strsplit(as.character(table[i,"Long"]),"+", fixed = T)[[1]]))
wide<-as.numeric(gsub(",",".",strsplit(as.character(table[i,"Wide"]),"+", fixed = T)[[1]]))
table[i,"Volume"]<-sum(sapply(1:length(long), function(x) (long[x]*wide[x]*wide[x])*(pi/6)))
}
dades$taula<-taula
dades$groups<-read.xlsx(input$file_sizes$datapath, sheet = 2, colNames=F)[,1]
table$Volume<-as.numeric(table$Volume)
dades$taula<-table
dades$groups<-read.xlsx(input$file_sizes$datapath, sheet = "Groups", colNames=F)[,1]
if (readxl::excel_sheets(input$file_sizes$datapath) %>% length > 2){
dades$sex<-read.xlsx(input$file_sizes$datapath, sheet = 3, sep.names = " ")
}
@ -127,7 +135,15 @@ server <- function(input, output) {
output$firstPlot <- renderPlot({
observeEvent(dades$taula, {})
if (!is.null(dades$taula)){
ggplot(dades$taula, aes(x="1", y=Volume))+geom_hline(yintercept = c(input$lowcut, input$upcut), color="red")+geom_quasirandom(width=0.2)
ggplot(dades$taula %>% filter(DayPostInoc == input$day_vol), aes(x="1", y=Volume))+
geom_hline(yintercept = c(input$lowcut, input$upcut), color="red")+
geom_quasirandom(width=0.2)
}
})
output$day_vol<-renderUI({
if (!is.null(dades$taula)){
selectInput("day_vol", "Día para volúmenes", choices = sort(unique(dades$taula$DayPostInoc)))
}
})
@ -138,15 +154,17 @@ server <- function(input, output) {
})
output$lowcut<-renderUI({
if (!is.null(dades$taula)){
cut.max<-round(max(dades$taula$Volume, na.rm = T), 2)
step<-round(max(dades$taula$Volume, na.rm = T)/100, 2)
taula<-dades$taula %>% filter(DayPostInoc == input$day_vol)
cut.max<-round(max(taula$Volume, na.rm = T), 2)
step<-round(max(taula$Volume, na.rm = T)/100, 2)
sliderInput("lowcut", "Corte inferior", min=0, max=cut.max, step=step, value=0)
}
})
output$upcut<-renderUI({
if (!is.null(dades$taula)){
cut.max<-round(max(dades$taula$Volume, na.rm = T), 2)+0.01
step<-round(max(dades$taula$Volume, na.rm = T)/20, 2)
taula<-dades$taula %>% filter(DayPostInoc == input$day_vol)
cut.max<-round(max(taula$Volume, na.rm = T), 2)+0.01
step<-round(max(taula$Volume, na.rm = T)/20, 2)
sliderInput("upcut", "Corte superior", min=0, max=cut.max, step=step, value=cut.max)
}
})
@ -167,11 +185,12 @@ server <- function(input, output) {
})
grafic<-eventReactive(input$goButton,{
df<-dades$taula
df<-dades$taula %>% filter(DayPostInoc == input$day_vol)
print(df)
df<-df[!is.na(df$Volume),]
up_cuttof<-input$upcut
low_cuttof<-input$lowcut
# print(up_cuttof)
df<-df[df$Volume < up_cuttof & df$Volume >= low_cuttof,]
if (is.null(dades$sex)){
df<-add_column(df, sex="undefined")
@ -179,16 +198,14 @@ server <- function(input, output) {
df<-merge(df, dades$sex)
}
# df["Mouse"]<-gsub("[a-zA-Z]", "", df$MouseID)
s<-shapiro.test(df$Volume)[[2]]
ngroup<-length(dades$groups)
df_def<-list()
# print(head(df))
for (sex.var in unique(df$sex)){
# print(sex.var)
df_sex<-df %>% filter(`sex` == sex.var)
ind.list<-list()
pval.list<-list()
@ -197,8 +214,9 @@ server <- function(input, output) {
for (data in 1:input$iterations){
interr=T
while(interr == T){
ind<-sample(rep(dades$groups, each=ceiling(length(unique(df_sex$`ID animal`))/ngroup)), length(unique(df_sex$`ID animal`)))
df_sex<-merge(df_sex[,c("ID animal", "ID tumor","Volume")], data.frame("ID animal"=unique(df_sex$`ID animal`), "group"=as.factor(ind),check.names=F))
ind<-sample(rep(dades$groups, each=ceiling(length(unique(df_sex$Animal))/ngroup)), length(unique(df_sex$Animal)))
df_sex<-merge(df_sex[,c("Animal", "Side","Volume")], data.frame("Animal"=unique(df_sex$Animal), "group"=as.factor(ind),check.names=F))
print(df_sex)
if ((nrow(df_sex)/ngroup) %% 2 == 0){
interr<-any(table(df_sex$group) < floor(nrow(df_sex)/ngroup) | table(df_sex$group) > ceiling(nrow(df_sex)/ngroup))
}else{
@ -206,7 +224,7 @@ server <- function(input, output) {
interr<-diff(range(table(ind))) > 1
}
}
ind.list[[data]]<-df_sex[,c("ID animal","ID tumor","group","Volume")]
ind.list[[data]]<-df_sex[,c("Animal","Side","group","Volume")]
lvn.list[data]<-leveneTest(Volume ~ group, data = df_sex[,3:4])[[2]][1]
if (s < 0.05){
k<-kruskal.test(df_sex$Volume,df_sex$group)
@ -229,23 +247,25 @@ server <- function(input, output) {
df_def<-df_def %>% select(-"Group")
}
df_def<-merge(
if(!is.null(dades$sex)){merge(dades$taula, dades$sex)}else{dades$taula %>% add_column(sex="undefined")} %>% select(-Group),
df_def[,c("ID animal", "group")] %>% unique, all=T, by="ID animal")
if("DPV" %in% colnames(df_def)){df_def<-select(df_def, c(`ID animal`, `sex`,`ID tumor`, Volume, Cage, Major, Minor, group))}
if("TS-Deep" %in% colnames(df_def)){df_def<-select(df_def, c(`ID animal`, `sex`,`ID tumor`, Volume, Cage, `TS-Deep`,`TS-Length`,`TS-Width`, group))}
if(!is.null(dades$sex)){merge(dades$taula %>% filter(DayPostInoc == input$day_vol), dades$sex)}else{
dades$taula %>% filter(DayPostInoc == input$day_vol) %>% add_column(sex="undefined")} %>% select(-Group),
df_def[,c("Animal", "group")] %>% unique, all=T, by="Animal") %>% rename(Group=group)
df_def<-select(df_def, Cage, Animal, Date, DayPostInoc, Group, Side, Weight, Long, Wide, Volume, Observations)
# if("DPV" %in% colnames(df_def)){df_def<-select(df_def, c(`ID animal`, `sex`,`ID tumor`, Volume, Cage, Major, Minor, group))}
# if("TS-Deep" %in% colnames(df_def)){df_def<-select(df_def, c(`ID animal`, `sex`,`ID tumor`, Volume, Cage, `TS-Deep`,`TS-Length`,`TS-Width`, group))}
df_def[!paste0(df_def$`ID animal`, df_def$`ID tumor`) %in% paste0(df$`ID animal`, df$`ID tumor`),"group"]<-NA
df_def[!paste0(df_def$Animal, df_def$Side) %in% paste0(df$Animal, df$Side),"Group"]<-NA
dades$db<-df_def
if (is.null(dades$sex)){
ggplot(df_def, aes(group, Volume))+
ggplot(df_def, aes(Group, Volume))+
geom_boxplot(outlier.alpha = F)+
geom_jitter(width=0.25)+
geom_point(stat="summary", color="blue", size=3)+
theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5))
}else{
ggarrange(
ggplot(df_def, aes(group, Volume))+
ggplot(df_def, aes(Group, Volume))+
geom_boxplot(outlier.alpha = F)+
geom_jitter(width=0.25, aes(color=sex))+
geom_point(stat="summary", color="blue", size=3)+
@ -255,7 +275,7 @@ server <- function(input, output) {
ggplot(df_def, aes(sex, Volume))+
geom_boxplot(outlier.alpha = F)+
geom_quasirandom(width=0.3),
ggplot(df_def, aes(group, fill=sex))+
ggplot(df_def, aes(Group, fill=sex))+
geom_bar(stat="count", color="black", position="dodge")+
guides(fill="none")+
theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5)), ncol = 1, heights = c(0.35, 0.65)),
@ -275,8 +295,8 @@ server <- function(input, output) {
observeEvent(dades$db, {})
if (!is.null(dades$db)){
df<-dades$db
df_sum<-dcast(df, group~., value.var = "Volume", fun.aggregate = mean, na.rm=T) %>% rename("Mean"=".")
df_sum["SEM"]<-dcast(df, group~., value.var = "Volume", fun.aggregate = std.error, na.rm=T) %>% pull(`.`)
df_sum<-dcast(df, Group~., value.var = "Volume", fun.aggregate = mean, na.rm=T) %>% rename("Mean"=".")
df_sum["SEM"]<-dcast(df, Group~., value.var = "Volume", fun.aggregate = std.error, na.rm=T) %>% pull(`.`)
df_sum
}
})
@ -284,7 +304,7 @@ server <- function(input, output) {
observeEvent(dades$db, {})
if (!is.null(dades$db)){
df<-dades$db
df %>% arrange(group)
df %>% arrange(Group)
}
})
@ -300,31 +320,12 @@ server <- function(input, output) {
# timepoint<-c(7,10,13,16,19,22,25)
if (!is.null(input$file_sizes)){
# dtemplate<-dades$db %>% select(-Volume,-sex)
# dtemplate<-melt(dtemplate, id=c("Cage", "ID animal", "ID tumor", "group"), variable.name = "DPV", value.name = "0") %>% rename("Group"="group")
# dtemplate<-dtemplate[,c("Cage", "ID animal", "ID tumor", "Group", "DPV", "0")] %>% arrange(`ID animal`, `ID tumor`)
# template<-expand.grid(dades$db$MouseID, timepoint)
# colnames(template)<-c("MouseID", "Timepoint")
# template<-template[order(template$Timepoint, template$MouseID),]
# template<-merge(template, dades$db[c("MouseID", "group")])
# if (input$measure_sys == "L-W-D"){
# template<-rbind(template, template, template)
# template<-template[order(template$Timepoint, template$MouseID),]
# template["TS"]<-rep(c("TS-Length", "TS-Width", "TS-Deep"), nrow(template)/3)
# dtemplate<-dcast(template, MouseID+group+TS~Timepoint)
# dtemplate<-dtemplate[mixedorder(as.character(dtemplate$MouseID)),]
# }
# if (input$measure_sys == "Min-Max"){
# template<-rbind(template, template)
# template<-template[order(template$Timepoint, template$MouseID),]
# template["DPV"]<-rep(c("Major", "Minor"), nrow(template)/2)
# dtemplate<-dcast(template, MouseID+group+DPV~Timepoint)
# dtemplate<-dtemplate[mixedorder(as.character(dtemplate$MouseID)),]
# }
# dtemplate<-dtemplate %>% add_column(.after="MouseID", "ID tumor"=dtemplate$MouseID)%>% rename(`ID animal`=MouseID)
# dtemplate["ID tumor"]<-gsub("[[:digit:]]","",dtemplate$`ID tumor`)
# dtemplate["ID animal"]<-gsub("[LR]","",dtemplate$`ID animal`)
# dtemplate[,5:ncol(dtemplate)]<-""
template<-dades$db %>% filter(!is.na(Group)) %>%
select(Animal, Group) %>% unique()
dtemplate<-merge(dades$taula %>% select(-Group), template) %>%
arrange(DayPostInoc, Animal, Side) %>%
select(Cage, Animal, Date, DayPostInoc, Group, Side,
Weight, Long, Wide, Volume, Observations)
}else{
template<-data.frame(

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