marcelcosta/invivos
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He añadido una pestaña para exportar imágenes. También he añadido el timepoint 0 cuando no existe para que los gráficos empiezen siempre en él.

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marcelcosta
2020-11-13 08:02:48 +01:00
parent 5019fab020
commit 19097d20dc
1 changed files with 107 additions and 2 deletions
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invivos/app.R
+107 -2
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@@ -45,7 +45,26 @@ ui <- fluidPage(
h3('Estadística'),
verbatimTextOutput('stats'),
tableOutput('tab_stats')
))
)),
tabPanel("Exportar",
sidebarPanel(width=2,
h3('Seleccionar figura'),
selectInput("fig_id", "", selected="", choices=c("Cinética Grupo", "Cinética Individual", "Survival")),
h3('Formato'),
sliderInput("width", "Ancho", min=1000, max=20000, step=1000, value=10000),
sliderInput("height", "Altura", min=1000, max=20000, step=1000, value=6000),
textInput("colors", label="Colors", value=""),
sliderInput("errorbar-width", "% Ancho errorbars", min=0.05, max=1, step=0.05, value=0.05),
sliderInput("point-size", "Tamaño puntos", min=1, max=10, step=1, value=3),
sliderInput("font-size", "Tamaño textos", min=5, max=30, step=1, value=11),
checkboxInput(inputId = "legend", label = "Mostrar llegenda", value = T),
selectInput("theme", "Seleccionar Tema", selected="BW", choices=c("BW", "Default", "Classic")),
downloadButton("downloadPicture", "Exportar")
),
mainPanel(
uiOutput("expPlotUI")
)
)
)
)
@@ -229,9 +248,12 @@ server <- function(input, output) {
if ("ID.tumor" %in% colnames(table)){table<-rename(table, "ID tumor"=`ID.tumor`)}
# table[table$ID.tumor == "R","0"]<-NA
col_nodays<-c("ID", "Cage","Group", "ID.animal","ID animal", "ID.tumor", "ID tumor", "TS","DPV", "Absorbance")
print(grep(0, colnames(table)[!colnames(table) %in% col_nodays]))
if (length(grep(0, colnames(table)[!colnames(table) %in% col_nodays])) == 0){
table["0"]<-0
}
table<-melt(table, id=colnames(table)[colnames(table) %in% col_nodays], variable.name = "Timepoint")
table$Timepoint<-gsub("[A-Za-z ]","",table$Timepoint)
table$Timepoint<-factor(table$Timepoint, levels=mixedsort(as.numeric(as.character(unique(table$Timepoint)))))
if ("DPV" %in% colnames(table)){
table<-dcast(table, Cage+`ID animal`+`ID tumor`+Group+Timepoint~DPV, value.var = "value")
table$Major<-table$Major/1000
@@ -244,6 +266,7 @@ server <- function(input, output) {
}
if (!"Volume" %in% colnames(table)){table<-rename(table, "Volume"=value)}
table<-table %>% filter(!is.na(Group))
table$Timepoint<-factor(table$Timepoint, levels=mixedsort(as.numeric(as.character(unique(table$Timepoint)))))
analysis$taula_def<-table
table_plot<-dcast(dcast(table %>% filter(!is.na(Volume)), `ID animal`+Group+Timepoint~., value.var = "Volume", fun.aggregate = mean), Group~Timepoint)
table_plot
@@ -373,6 +396,88 @@ server <- function(input, output) {
}
}
})
output$expPlotUI<- renderUI({
observeEvent(analysis$taula_def, {})
if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
plotOutput("expPlot", width=paste0(input$width/10,"px"), height = paste0(input$height/10, "px"))
}
})
output$expPlot <- renderPlot({
observeEvent(analysis$taula_def, {})
if (!is.null(input$file_analy) & !is.null(analysis$taula_def)){
table<-analysis$taula_def
print(head(table))
if (input$fig_id == "Cinética Grupo"){
if (input$vacc == "Sí"){
g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=Group))+
scale_x_continuous(expand = expansion(mult = c(0,0.05)), limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~., scale="free_y")+
theme_bw()
}else{
g<-ggplot(table, aes(Timepoint, Volume, color=Group, group=Group))+
theme_bw()
}
}
if (input$fig_id == "Cinética Individual"){
if (input$vacc == "Sí"){
g<-ggplot(table, aes(as.numeric(as.character(Timepoint)), Volume, color=Group, group=Group))+
scale_x_continuous(expand = expansion(mult = c(0,0.05)), limits = c(0, (round(max(as.numeric(as.character(table$Timepoint))) / 5)+1)*5))+
facet_grid(factor(`ID tumor`, labels = c("Vaccination", "Rechallenge"))~Group, scale="free_y")+
theme_bw()
}else{
g<-ggplot(table, aes(Timepoint, Volume, color=Group, group=`ID animal`))+
facet_wrap(.~Group)+
theme_bw()
}
}
g<-g+geom_errorbar(stat="summary", width=input$`errorbar-width`)+
geom_line(stat="summary")+
geom_point(stat="summary", size=input$`point-size`)+
labs(x="Days after tumor challenge")+
scale_y_continuous(expand = expansion(mult = c(0,0.05)))
if (input$theme == "BW"){
g<-g+theme_bw(base_size = input$`font-size`)
}
if (input$theme == "Classic"){
g<-g+theme_classic(base_size = input$`font-size`)
}
if (input$theme == "Default"){
g<-g+theme_gray(base_size = input$`font-size`)
}
# g<-g+theme(axis.text.x=element_text(angle=45, hjust=1))
if (input$legend == F){
g<-g+guides(color=FALSE, fill=FALSE)
}
if (input$colors != ""){
v_col<-strsplit(input$colors, ",")[[1]]
g<-g+scale_color_manual(values=v_col)+
scale_fill_manual(values=v_col)
}
dades$plot<<-g
g
}
}, res=72)
output$downloadPicture <- downloadHandler(
filename = function() {
paste("Figura", ".png", sep="")
},
content = function(file){
print(file)
# tempReport <- file.path(tempdir(), "elispots.Rmd")
# file.copy("elispots.Rmd", tempReport, overwrite = TRUE)
png(file, width = input$width, height=input$height, units = "px", res=720)
plot(dades$plot)
dev.off()
})
}
# Run the application