regionplot

library(topr)

Single GWAS

To display a region around a given gene:

regionplot(CD_UKBB, gene="IL23R")

[1] "Zoomed to region:  1:67038907-67359979"

Or alternatively, use the region argument to display the region:

regionplot(CD_UKBB, region="1:67038907-67359979")

[1] "Zoomed to region:  1:67038907-67359979"

Label the top marker

regionplot(CD_UKBB, gene="IL23R", annotate=5e-9)

[1] "Zoomed to region:  1:67038907-67359979"

Annotate the top marker per 100000 bp region (region_size=100000) and further highlight the marker position with a vertical line. Move the marker id’s slightly up and towards the right (nudge_y=1 and nudge_x=25000).

regionplot(CD_UKBB, gene="IL23R", annotate_with_vline = 5e-8, region_size = 100000, nudge_y=1, nudge_x=25000)

[1] "Zoomed to region:  1:67038907-67359979"

Multi GWAS

regionplot(list(CD_UKBB, CD_FINNGEN), gene="IL23R")

[1] "Use the legend_labels argument to change the legend labels from color names to meaningful labels! "
[1] "Zoomed to region:  1:67038907-67359979"

regionplot(list(CD_UKBB, CD_FINNGEN), gene="IL23R", annotate_with_vline =5e-08, color=c("#7D7D7D","darkred"), legend_labels = c("UKBB", "FinnGen"), show_gene_legend = F, protein_coding_only = T, gene_color="#646464")

[1] "Zoomed to region:  1:67038907-67359979"