marcelcosta/invivos
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Corregir asignador de grupos

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Costa
2020-12-22 15:20:27 +01:00
parent 4500068b85
commit 41512dd8b4
1 changed files with 60 additions and 39 deletions
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invivos/app.R
+60 -39
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@@ -84,14 +84,24 @@ server <- function(input, output) {
dades$db<-NULL dades$db<-NULL
observe({ observe({
if (!is.null(input$file_sizes)){ if (!is.null(input$file_sizes)){
dades$taula<-read.xlsx(input$file_sizes$datapath, sheet = 1) taula<-read.xlsx(input$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$Minor)*(pi/6))
}
dades$taula<-taula
dades$groups<-read.xlsx(input$file_sizes$datapath, sheet = 2)[,1] dades$groups<-read.xlsx(input$file_sizes$datapath, sheet = 2)[,1]
} }
}) })
output$firstPlot <- renderPlot({ output$firstPlot <- renderPlot({
observeEvent(dades$taula, {}) observeEvent(dades$taula, {})
if (!is.null(dades$taula)){ if (!is.null(dades$taula)){
ggplot(dades$taula, aes(x="1", y=Volumen))+geom_quasirandom(width=0.2) ggplot(dades$taula, aes(x="1", y=Volume))+geom_quasirandom(width=0.2)
} }
}) })
@@ -124,13 +134,14 @@ server <- function(input, output) {
df<-dades$taula df<-dades$taula
up_cuttof<-input$upcut up_cuttof<-input$upcut
low_cuttof<-input$lowcut low_cuttof<-input$lowcut
df<-df[df$Volumen < up_cuttof & df$Volumen > low_cuttof,] df<-df[df$Volume <= up_cuttof & df$Volume >= low_cuttof,]
df["Mouse"]<-gsub("[a-zA-Z]", "", df$MouseID)
s<-shapiro.test(df$Volumen)[[2]]
# df["Mouse"]<-gsub("[a-zA-Z]", "", df$MouseID)
print(df$Volume)
s<-shapiro.test(df$Volume)[[2]]
ngroup<-length(dades$groups) ngroup<-length(dades$groups)
ind.list<-list() ind.list<-list()
pval.list<-list() pval.list<-list()
lvn.list<-list() lvn.list<-list()
@@ -138,32 +149,39 @@ server <- function(input, output) {
for (data in 1:input$iterations){ for (data in 1:input$iterations){
interr=T interr=T
while(interr == T){ while(interr == T){
ind<-sample(rep(dades$groups, each=7), length(unique(df$Mouse))) ind<-sample(rep(dades$groups, each=ceiling(length(unique(df$`ID animal`))/ngroup)), length(unique(df$`ID animal`)))
df_temp<-merge(df, data.frame("Mouse"=unique(df$Mouse), "group"=as.factor(ind))) df_temp<-merge(df[,c("ID animal", "ID tumor","Volume")], data.frame("ID animal"=unique(df$`ID animal`), "group"=as.factor(ind),check.names=F))
interr<-any(table(df_temp$group) < floor(nrow(df_temp)/5) | table(df_temp$group) > ceiling(nrow(df_temp)/5)) if ((nrow(df_temp)/ngroup) %% 2 == 0){
interr<-any(table(df_temp$group) < floor(nrow(df_temp)/ngroup) | table(df_temp$group) > ceiling(nrow(df_temp)/ngroup))
}else{
interr<-any(table(df_temp$group) < (floor(nrow(df_temp)/ngroup)-1) | table(df_temp$group) > (ceiling(nrow(df_temp)/ngroup)+1))
} }
ind.list[[data]]<-df_temp[,c("MouseID","group")] }
lvn.list[data]<-leveneTest(Volumen ~ group, data = df_temp[,3:4])[[2]][1] ind.list[[data]]<-df_temp[,c("ID animal", "ID tumor","group","Volume")]
lvn.list[data]<-leveneTest(Volume ~ group, data = df_temp[,3:4])[[2]][1]
if (s < 0.05){ if (s < 0.05){
k<-kruskal.test(df_temp$Volumen,df_temp$group) k<-kruskal.test(df_temp$Volume,df_temp$group)
test.list[data]<-k[[1]][1] test.list[data]<-k[[1]][1]
pval.list[data]<-k[[3]][1] pval.list[data]<-k[[3]][1]
}else{ }else{
res.aov<-aov(Volumen~group, data=df_temp) res.aov<-aov(Volume~group, data=df_temp)
pval.list[data]<-summary(res.aov)[[1]][[5]][1] pval.list[data]<-summary(res.aov)[[1]][[5]][1]
test.list[data]<-summary(res.aov)[[1]][[4]][1] test.list[data]<-summary(res.aov)[[1]][[4]][1]
} }
} }
index<-which(unlist(lvn.list) == min(unlist(lvn.list)[which(unlist(pval.list) %in% sort(unlist(pval.list), decreasing = T)[1:20])])) index<-which(unlist(lvn.list) == min(unlist(lvn.list)[which(unlist(pval.list) %in% sort(unlist(pval.list), decreasing = T)[1:20])]))
df_def<-merge(df, ind.list[[index]]) df_def<-merge(df, ind.list[[index]])
if ("Group" %in% colnames(df_def)){
df_def<-df_def %>% select(-"Group")
}
dades$db<-df_def dades$db<-df_def
print(df_def)
ggplot(df_def, aes(group, Volumen))+ ggplot(df_def, aes(group, Volume))+
geom_boxplot(outlier.alpha = F)+ geom_boxplot(outlier.alpha = F)+
geom_jitter(width=0.25)+ geom_jitter(width=0.25)+
geom_point(stat="summary", color="blue", size=3)+ geom_point(stat="summary", color="blue", size=3)
lims(y=c(0,max(df_def$Volumen)+10)) # lims(y=c(0,max(df_def$Volume)+10))
}) })
output$distPlot <- renderPlot({ output$distPlot <- renderPlot({
observeEvent(dades$taula, {}) observeEvent(dades$taula, {})
@@ -184,28 +202,31 @@ server <- function(input, output) {
timepoint<-c(7,10,13,16,19,22,25) timepoint<-c(7,10,13,16,19,22,25)
if (!is.null(input$file_sizes)){ if (!is.null(input$file_sizes)){
template<-expand.grid(dades$db$MouseID, timepoint) dtemplate<-df$db %>% select(-Volume)
colnames(template)<-c("MouseID", "Timepoint") dtemplate<-melt(dtemplate, id=c("Cage", "ID animal", "ID tumor", "group"), variable.name = "DPV", value.name = "0") %>% rename("Group"="group")
template<-template[order(template$Timepoint, template$MouseID),] dtemplate<-dtemplate[,c("Cage", "ID animal", "ID tumor", "Group", "DPV", "0")]
template<-merge(template, dades$db[c("MouseID", "group")]) # template<-expand.grid(dades$db$MouseID, timepoint)
if (input$measure_sys == "L-W-D"){ # colnames(template)<-c("MouseID", "Timepoint")
template<-rbind(template, template, template) # template<-template[order(template$Timepoint, template$MouseID),]
template<-template[order(template$Timepoint, template$MouseID),] # template<-merge(template, dades$db[c("MouseID", "group")])
template["TS"]<-rep(c("TS-Length", "TS-Width", "TS-Deep"), nrow(template)/3) # if (input$measure_sys == "L-W-D"){
dtemplate<-dcast(template, MouseID+group+TS~Timepoint) # template<-rbind(template, template, template)
dtemplate<-dtemplate[mixedorder(as.character(dtemplate$MouseID)),] # template<-template[order(template$Timepoint, template$MouseID),]
} # template["TS"]<-rep(c("TS-Length", "TS-Width", "TS-Deep"), nrow(template)/3)
if (input$measure_sys == "Min-Max"){ # dtemplate<-dcast(template, MouseID+group+TS~Timepoint)
template<-rbind(template, template) # dtemplate<-dtemplate[mixedorder(as.character(dtemplate$MouseID)),]
template<-template[order(template$Timepoint, template$MouseID),] # }
template["DPV"]<-rep(c("Major", "Minor"), nrow(template)/2) # if (input$measure_sys == "Min-Max"){
dtemplate<-dcast(template, MouseID+group+DPV~Timepoint) # template<-rbind(template, template)
dtemplate<-dtemplate[mixedorder(as.character(dtemplate$MouseID)),] # template<-template[order(template$Timepoint, template$MouseID),]
} # template["DPV"]<-rep(c("Major", "Minor"), nrow(template)/2)
dtemplate<-dtemplate %>% add_column(.after="MouseID", "ID tumor"=dtemplate$MouseID)%>% rename(`ID animal`=MouseID) # dtemplate<-dcast(template, MouseID+group+DPV~Timepoint)
dtemplate["ID tumor"]<-gsub("[[:digit:]]","",dtemplate$`ID tumor`) # dtemplate<-dtemplate[mixedorder(as.character(dtemplate$MouseID)),]
dtemplate["ID animal"]<-gsub("[LR]","",dtemplate$`ID animal`) # }
dtemplate[,5:ncol(dtemplate)]<-"" # 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)]<-""
}else{ }else{
template<-expand.grid(LETTERS[1:ncages], 1:5, id_tumors, timepoint)[,-2] template<-expand.grid(LETTERS[1:ncages], 1:5, id_tumors, timepoint)[,-2]
colnames(template)<-c("Cage", "ID tumor", "Timepoint") colnames(template)<-c("Cage", "ID tumor", "Timepoint")