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server.R
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shinyServer(function(input, output, session) {
js$collapseNodesOnLoad()
js$log2Slider(id = "Age", max_power = log2(age_max))
output$nt_tree <- renderTree({
list(All = structure(region_groups,stselected = TRUE,stopened= TRUE))
})
output$species_tree <- renderTree({
list(All = structure(list(Mice = structure("Mice",stselected=TRUE),
Rats = structure("Rats",stselected=TRUE),
Others = structure(as.list(setNames(misc_species,misc_species)),stselected = TRUE)),stopened=TRUE))
})
values <- reactiveValues(selected = rep(1, nrow(bigData)))
removed <- reactiveValues(selected = rep(FALSE,nrow(bigData)))
observeEvent(input$toggle1,{
js$removeStuckToolTip()
})
observeEvent(input$clearance, {
values$selected <- rep(1,nrow(bigData))
js$removeStuckToolTip()
})
observeEvent(input$restoreRemoved, {
removed$selected <- rep(FALSE,nrow(bigData))
})
observeEvent(input$remove, {
removed$selected <- unlist(lapply(values$selected,function(x){
if (x == 1){
FALSE
} else {
TRUE
}
}))
}
)
make_main_plot <- function(df, x_axis, y_axis){
data_frame <- df()
x_axis_col <- as.character(x_axis())
y_axis_col <- as.character(y_axis())
x_axis_lab <- x_axis_col
y_axis_lab <- y_axis_col
#filter out NA values
if (y_axis_lab == "---") {
data_frame <- data_frame %>% filter(!is.na(data_frame[,x_axis_lab]))
}
else {
data_frame <- data_frame %>% filter(!is.na(data_frame[,x_axis_lab]) & !is.na(data_frame[,y_axis_lab]))
}
# Add units for ephys props and relevant metadata
if (x_axis_lab %in% rownames(props)) {
x_axis_lab <- paste(x_axis_lab, " (", props[[x_axis_lab,c("usual.units")]], ")")
}
else if (x_axis_lab %in% names(metadata_units)) {
x_axis_lab <- paste(x_axis_lab, " (", metadata_units[x_axis_lab], ")")
}
# Add units for ephys props
if (y_axis_lab %in% rownames(props)) {
y_axis_lab <- paste(y_axis_lab, " (", props[[y_axis_lab,c("usual.units")]], ")")
}
else if (y_axis_lab %in% names(metadata_units)) {
y_axis_lab <- paste(y_axis_lab, " (", metadata_units[y_axis_lab], ")")
}
# Just one variable selected - show frequency bars
if (y_axis_lab == "---") {
# No data - make an empty plot
if (nrow(data_frame) == 0) {
data_frame %>% ggvis(x=x_axis(),y=x_axis()) %>% layer_points() %>%
add_axis('y', title = "Count", properties = axis_props(labels=list(angle = -40,fontSize=10),title=list(fontSize=16,dy = -55)))%>%
add_axis('x', title = x_axis_lab, properties = axis_props(labels=list(angle = -40,fontSize=10, dx = -30,dy=5),title=list(fontSize=16,dy = 50)))
}
# Categorical - make a frequency bar chart
else if (!is.numeric(data_frame[,x_axis_col])) {
data_frame %>% ggvis(x=x_axis()) %>% layer_bars() %>%
add_axis('y', title = "Count", properties = axis_props(labels=list(angle = -40,fontSize=10),title=list(fontSize=16,dy = -55)))%>%
add_axis('x', title = x_axis_lab, properties = axis_props(labels=list(angle = -40,fontSize=10, dx = -30,dy=5),title=list(fontSize=16,dy = 50)))
}
# Continous - make a histogram
else {
data_frame %>% ggvis(x=x_axis()) %>% layer_histograms() %>%
add_axis('y', title = "Count", properties = axis_props(labels=list(angle = -40,fontSize=10),title=list(fontSize=16,dy = -55)))%>%
add_axis('x', title = x_axis_lab, properties = axis_props(labels=list(angle = -40,fontSize=10, dx = -30,dy=5),title=list(fontSize=16,dy = 50)))
}
}
# Both variables categorical - make a frequency matrix
else if (!is.numeric(data_frame[,x_axis_col]) && !is.numeric(data_frame[,y_axis_col])) {
# No data - make an empty plot
if (nrow(data_frame) == 0) {
data_frame %>% ggvis(x=x_axis(),y=x_axis()) %>% layer_points() %>%
add_axis('y', title = y_axis_lab, properties = axis_props(labels=list(angle = -40,fontSize=10),title=list(fontSize=16,dy = -70)))%>%
add_axis('x', title = x_axis_lab, properties = axis_props(labels=list(angle = -40,fontSize=10, dx = -30,dy=5),title=list(fontSize=16,dy = 70)))
}
else {
form <- as.formula(paste("~",x_axis_col,"+",y_axis_col))
freqs <- melt(xtabs(form, data_frame))
freqs%>%
ggvis(x=x_axis(), y=y_axis(), fill=~value)%>%
layer_rects(width = band(), height = band()) %>%
layer_text(
x = prop("x", x_axis(), scale = "xcenter"),
y = prop("y", y_axis(), scale = "ycenter"),
text:=~value, fontSize := 14, fill:="white", baseline:="middle", align:="center") %>%
scale_nominal("x", padding = 0, points = FALSE) %>%
scale_nominal("y", padding = 0, points = FALSE) %>%
scale_nominal("x", name = "xcenter", padding = 1, points = TRUE) %>%
scale_nominal("y", name = "ycenter", padding = 1, points = TRUE) %>%
add_axis('y', title = y_axis_lab, properties = axis_props(labels=list(angle = -40,fontSize=10),title=list(fontSize=16,dy = -70)))%>%
add_axis('x', title = x_axis_lab, properties = axis_props(labels=list(angle = -40,fontSize=10, dx = -30,dy=5),title=list(fontSize=16,dy = 70)))
}
}
# Both variables continous - make a scatterplot
else {
format_x <- if (x_axis_col == "PubYear") "####" else ""
format_y <- if (y_axis_col == "PubYear") "####" else ""
data_frame %>%
ggvis(x =x_axis(), y= y_axis(), key := ~key, fill = ~col, size = ~col ) %>%
hide_legend(scales = c('fill','size')) %>%
add_axis('y',title = y_axis_lab, format = format_y, properties = axis_props(labels=list(angle = -40,fontSize=10),title=list(fontSize=16,dy = -55)))%>%
add_axis('x', title = x_axis_lab, format = format_x, properties = axis_props(labels=list(angle = -40,fontSize=10, dx = -30,dy=5),title=list(fontSize=16,dy = 50)))%>%
layer_points() %>%
set_options(height = 400, width = 600) -> stuff
if (x_axis_col %in% log_transform) {
stuff %>% scale_numeric("x", trans="log", expand=0) -> stuff
}
if (y_axis_col %in% log_transform) {
stuff %>% scale_numeric("y", trans="log", expand=0) -> stuff
}
stuff %>%
add_tooltip(function(data){
paste0(
'Title :',data_frame[data_frame$key == data$key,'Title'],"<br>",'PubMed ID: ', data_frame[data_frame$key == data$key,'Pmid'],"<br>",
x_axis(),": ", as.character(data[[1]]), "<br>", y_axis(), ": ", as.character(data[[2]]),"<br>")
}
, "hover")%>%
set_options(renderer = "canvas") %>%
handle_click(on_click = function(data,...){
isolate(values$selected[data$key] <- 2)
}
) #ggvis-tooltip
}
}
mtc <- reactive({
data = bigData
# Apply filters (only on attributes where not everything is selected)
if (!is.null(input$nt_tree)) {
selected_nts <- get_selected(input$nt_tree)
selected_nts <- selected_nts[!(selected_nts %in% c("All",regions))]
if (length(selected_nts) < nrow(neuron_types)){
data <- data[data$NeuronName %in% selected_nts,]
}
}
if (!is.null(input$species_tree)) {
selected_species <- get_selected(input$species_tree)
selected_species <- selected_species[!(selected_species %in% c("All","Others"))]
if (length(selected_species) < length(species)){
data <- data[data$Species %in% selected_species,]
}
}
age_slider_min <- input$Age[1]
age_slider_max <- input$Age[2]
age_low <- if (age_slider_min == 0) 0 else (2^(age_slider_min - 1))
age_high <- if (age_slider_max == 0) 0 else (2^(age_slider_max - 1))
if (age_low > 0 || age_high < age_max) {
data <- data[which(!is.na(data$AnimalAge) & data$AnimalAge >= age_low & data$AnimalAge <= age_high),]
}
temp_low <- input$Temperature[1]
temp_high <- input$Temperature[2]
if (temp_low > floor(min(temp)) || temp_high < ceiling(max(temp))) {
data <- data[which(!is.na(data$RecTemp) & data$RecTemp >= temp_low & data$RecTemp <= temp_high),]
}
weight_low <- input$Weight[1]
weight_high <- input$Weight[2]
if (weight_low > floor(min(weight)) || weight_high < ceiling(max(weight))) {
data <- data[which(!is.na(data$AnimalWeight) & data$AnimalWeight >= weight_low & data$AnimalWeight <= weight_high),]
}
for (x in rownames(props)) {
if (!is.null(input[[x]])) {
slider_val = input[[x]]
if (slider_val[1] > props[[x,c("Min.Range")]] || slider_val[2] < props[[x,c("Max.Range")]]) {
data <- data[which(!is.na(data[[x]]) & data[[x]] >= slider_val[1] & data[[x]] <= slider_val[2]),]
}
}
}
data$col <- values$selected[data$key]
data[!removed$selected[data$key],]
})
x1 <- reactive({as.symbol(input$x1)})
x2 <- reactive({as.symbol(input$x2)})
x3 <- reactive({as.symbol(input$x3)})
x4 <- reactive({as.symbol(input$x4)})
y1 <- reactive({as.symbol(input$y1)})
y2 <- reactive({as.symbol(input$y2)})
y3 <- reactive({as.symbol(input$y3)})
y4 <- reactive({as.symbol(input$y4)})
reactive({make_main_plot(mtc,x1,y1)})%>%
bind_shiny('plot1')
reactive({make_main_plot(mtc,x2,y2)})%>%
bind_shiny('plot2')
reactive({make_main_plot(mtc,x3,y3)})%>%
bind_shiny('plot3')
reactive({make_main_plot(mtc,x4,y4)})%>%
bind_shiny('plot4')
htc <- reactiveValues(keys = 1)
observe({
if (length(mtc()$key)!=length(htc$keys)){
htc$keys <<- mtc()$key
m <- bigData[which(bigData$key %in% htc$keys),]
output$hivePlot <- renderPlot({makeHivePlot(m)})
output$freqMat <- renderPlot({make_frequency_matrix(htc$keys)})
tab <- m[,c('Pmid','PubYear','LastAuthor','Title','allNeurons','allSpecies')]
output$table <-renderDataTable(tab[!duplicated(tab),],class ='compact cell-border stripe', filter = 'top', colnames = c('PubMed ID', 'Year','Author', 'Title','Neurons', 'Species'),rownames = FALSE)
}
} )
})