Welcome in the PCTG R Markdown template. This document describes how the template looks like, building an interactive Manhattan plot.
Let’s load a GWAS summary statistic stored in the qqman library. This library is:
library(qqman)
It’s often handy to keep a trace of the raw data somewhere in your document. The DT library allows to build interactive tables that you can search, filter, highlight and more.
library(DT)
datatable(gwasResults, rownames = FALSE, filter="top", options = list(pageLength = 5, scrollX=T) )
Using HTML
outputs you can embed some interactive graphics. For example, the plotly library can transform any of your ggplot2 graphic in an interactive chart:
# Make the plot
p <- ggplot(don, aes(x=BPcum, y=-log10(P), text=text)) +
# Show all points
geom_point( aes(color=as.factor(CHR)), alpha=0.8, size=1.3) +
scale_color_manual(values = rep(c("grey", "#563986"), 22 )) +
# custom X axis:
scale_x_continuous( label = axisdf$CHR, breaks= axisdf$center ) +
scale_y_continuous(expand = c(0, 0) ) + # remove space between plot area and x axis
# Add highlighted points
geom_point(data=subset(don, is_highlight=="yes"), color="orange", size=2) +
# Custom the theme:
theme_bw() +
theme(
legend.position="none",
panel.border = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank()
) +
ylim(0, 10)
ggplotly(p, tooltip="text")
A work by Yan Holtz