johrpan/ubigen
1
0
Fork 0
mirror of https://github.com/johrpan/ubigen.git synced 2025-10-26 19:57:24 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions

gsea: Categorize by GO subsection

Browse source
This commit is contained in:
Elias Projahn 2022-06-22 12:36:14 +02:00
parent ba1f9f3a7b
commit 989655307b
1 changed files with 18 additions and 6 deletions
Download patch file Download diff file Expand all files Collapse all files

24
scripts/gsea.R
View file

@ -20,23 +20,35 @@ result <- if (file.exists(file_path)) {
data[, bucket := ceiling(rank / bucket_size)] data[, bucket := ceiling(rank / bucket_size)]
result <- data[, .(analysis = list(gprofiler2::gost(gene))), by = bucket] result <- data[, .(analysis = list(gprofiler2::gost(gene))), by = bucket]
result[, count := nrow(analysis[[1]]$result), by = bucket]
result[is.na(count), count := 0]
saveRDS(result, file = file_path) saveRDS(result, file = file_path)
result result
} }
result[, result := lapply(analysis, function (a) a$result)]
result <- result[, rbindlist(result), by = bucket]
result <- result[source %chin% c("GO:CC", "GO:BP", "GO:MF")]
result[source == "GO:CC", label := "Cellular component"]
result[source == "GO:BP", label := "Biological pathway"]
result[source == "GO:MF", label := "Molecular function"]
data <- result[,
.(count = .N, label = unique(label)),
by = c("bucket", "source")
]
fig <- plotly::plot_ly() |> fig <- plotly::plot_ly() |>
plotly::add_bars( plotly::add_bars(
data = result, data = data,
x = ~bucket, x = ~bucket,
y = ~count y = ~count,
color = ~label
) |> ) |>
plotly::layout( plotly::layout(
xaxis = list(title = "Bucket of genes (n = 500)"), xaxis = list(title = "Bucket of genes (n = 500)"),
yaxis = list(title = "Number of associated terms") yaxis = list(title = "Number of associated terms"),
barmode = "stack"
) )
plotly::save_image(fig, image_path, width = 1200, height = 800) plotly::save_image(fig, image_path, width = 1200, height = 800)