10. Scatter plot with dropdown menus • plotlyvignettes

suppressPackageStartupMessages({
    library("plotlyutils")
    library("SummarizedExperiment")
    library("limma")
})

data(voomed_GBM, package="plotlyvignettes")
data(GBMdata, package="plotlyvignettes")
pcs <- prcomp(t(voomed_GBM$E))
pc_data <- pcs$x

columns <- c(
    "paper_IDH.status",
    "paper_Age..years.at.diagnosis.",
    "paper_Gender",
    "paper_Pan.Glioma.RNA.Expression.Cluster",
    "ethnicity"
)
colours <- colData(GBMdata)[, columns, drop = FALSE]
colours <- as.data.frame(colours)
colours$TotalReads <- colSums(assay(GBMdata))


plot(
    pc_data[, 1], 
    pc_data[, 2], 
    col = as.factor(colours[[1]]),
    pch = 16,
    xlab = "PC1",
    ylab = "PC2")
legend(
    max(pc_data[, 1]) * 0.7,
    max(pc_data[, 2]) * 0.7,
    unique(colours[[1]]),
    pch = 16,
    col = unique(colours[[1]]))

selectable_scatter_plot(pc_data, colours)