suppressPackageStartupMessages({
library("plotlyutils")
library("plotly")
})
data(GBMtopTable, package="plotlyvignettes")
set.seed(42)
tt <- GBMtopTable[sample(seq_len(nrow(GBMtopTable)), 1000), ]
title <- "Glioblastoma - IDH1 mutant vs wt"
xtitle <- "log<sub>2</sub>(fold-change)"
ytitle <- "-log<sub>10</sub>(FDR-adjusted p-value)"
colours <- c("#0000ff", "#000000", "#ff0000")
plot_ly(tt,
x = ~logFC,
y = ~-log10(P.Value),
color = ~ Group,
text = ~ Symbol,
hoverinfo = "x+y+text",
type = "scatter",
mode = "markers") %>%
layout(title = "Glioblastoma - IDH1 mutant vs wt",
xaxis = list(title = xtitle),
yaxis = list(title = ytitle))
linked_scatter_plot(
x = tt[["logFC"]],
xlab = xtitle,
y = -log10(tt[["adj.P.Val"]]),
ylab = ytitle,
xlim = c(-max(abs(tt[["logFC"]])), max(abs(tt[["logFC"]]))) * 1.1,
text = tt[["Text"]],
links = tt[["Links"]],
groups = tt[["Group"]],
title = title,
colours = colours)