Data Integration and Visualization on 'WikiPathways' Graphics

Retrieves pathway graphics from 'WikiPathways' and maps user-supplied quantitative data, such as gene expression values, onto pathway nodes. Provides a pipe-friendly grammar for building pathway visualizations with layered fills, text highlighting, condition-wise comparisons, data preparation helpers, and batch rendering utilities.

library(clusterProfiler)
library(wikiprofiler)

data(geneList, package="DOSE")

de <- names(geneList)[1:100]
x <- enrichWP(de, organism='Homo sapiens')


de2 <- bitr(de, "ENTREZID", "SYMBOL", OrgDb='org.Hs.eg.db')
#### if needed
# de2 <- de2[!duplicated(de2[,1]), ]
value <- setNames(geneList[de2[,1]], de2[,2])

ID <- x$ID[1]

p1 <- wpplot(ID)
p1

p2 <- p1 |> wp_bgfill(value, low='darkgreen', high='firebrick', legend_x = .9, legend_y = .95)
p2

p3 <- p2 |> wp_shadowtext()
p3