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volcano.R
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volcano.R
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# volcano table -----------------------------------------------------------
output$volcanoTable <- renderDataTable({
filtered = filterData()
if(!is.null(filtered)){ # check object exists
if(! 'expr' %in% colnames(filtered)) { # checks if the data has finished being transformed to a wide format
filtered = filtered %>%
mutate(FC = signif(FC, 3),
logFC = signif(logFC, 3),
logQ = signif(logQ, 3))
brushedPoints(filtered, input$volcanoBrush)
# Check if there's brushing activated. If not, display all.
brush <- input$volcanoBrush
if (!is.null(brush)) {
brushedPoints(filtered, brush) # Highlight only those brushed
} else if(!is.null(ranges$x)){ # After double click; highlight those w/i plot window
filtered %>%
filter(logFC >= ranges$x[1], logFC <= ranges$x[2],
logQ >= ranges$y[1], logQ <= ranges$y[2])
} else {
filtered
}
}
}
},
escape = c(-1,-2, -3),
options = list(searching = TRUE, stateSave = TRUE,
pageLength = 25,
rowCallback = JS(
'function(nRow, aData, iDisplayIndex, iDisplayIndexFull) {
if (aData[0])
$("td:eq(0)", nRow).css("color", "#293C97");
$("td", nRow).css("text-align", "center");
}')
)
)
# ggplot zoom -------------------------------------------------------------
# When a double-click happens, check if there's a brush on the plot.
# If so, zoom to the brush bounds; if not, reset the zoom.
# Code from RStudio (thanks, guys) http://shiny.rstudio.com/gallery/plot-interaction-zoom.html
# Single zoomable plot (on left)
ranges <- reactiveValues(x = NULL, y = NULL)
# When a double-click happens, check if there's a brush on the plot.
# If so, zoom to the brush bounds; if not, reset the zoom.
observeEvent(input$volcanoDblclick, {
brush <- input$volcanoBrush
if (!is.null(brush)) {
ranges$x <- c(brush$xmin, brush$xmax)
ranges$y <- c(brush$ymin, brush$ymax)
} else {
ranges$x <- NULL
ranges$y <- NULL
}
})
# Muscle selection boxes --------------------------------------------------
output$m1 = renderUI(
selectInput('muscle1', label = 'sample 1',
choices = input$muscles,
width = '200px'))
output$m2 = renderUI(
selectInput('muscle2', label = 'samplele 2 (reference)',
choices = input$muscles,
width = '200px'))
# volcano tooltip ---------------------------------------------------------
# ggvis volcano output ----------------------------------------------------
output$volcanoPlot <- renderPlot({
withProgress(message = 'Making plot', value = 0, {
filteredData = filterData()
incProgress(amount = 0.5)
if(!is.null(filteredData)){ # check object exists
if(! 'expr' %in% colnames(filteredData)) { # checks if the data has finished being transformed to a wide format
# Temporary plot to be replaced by interactive version.
ggplot(filteredData, aes(y = logQ, x = logFC)) +
geom_point(size = 3, alpha = 0.3, colour = 'dodgerblue') +
coord_cartesian(xlim = ranges$x, ylim = ranges$y) +
theme(title = element_text(size = 32, color = grey90K),
axis.line = element_blank(),
axis.ticks = element_blank(),
axis.text = element_text(size = 16, color = grey60K),
axis.title = element_text(size = 18, color = grey60K),
legend.position="none",
panel.grid.major = element_line(color = grey60K, size = 0.2),
panel.border = element_blank(),
plot.margin = rep(unit(0, units = 'points'),4),
panel.background = element_blank(),
strip.text = element_text(size=13, face = 'bold', color = grey60K),
strip.background = element_blank()
)
}
}
})
})
# Save volcano csv --------------------------------------------------------
output$csvVolcano <- downloadHandler(
filename = function() {
paste('volcano_data-', Sys.Date(), '.csv', sep='')
},
content = function(file) {
filteredData = filterData()
write.csv(filteredData, file)
}
)