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gsea: Show all sources in plot

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This commit is contained in:
Elias Projahn 2022-06-22 19:07:15 +02:00
parent 4cb08de325
commit af364b1da8
1 changed files with 4 additions and 11 deletions
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15
scripts/gsea.R
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@ -28,27 +28,20 @@ result <- if (file.exists(file_path)) {
result[, result := lapply(analysis, function (a) a$result)] result[, result := lapply(analysis, function (a) a$result)]
result <- result[, rbindlist(result), by = bucket] result <- result[, rbindlist(result), by = bucket]
result <- result[source %chin% c("GO:CC", "GO:BP", "GO:MF")] data <- result[, .(count = .N), by = c("bucket", "source")]
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 = data, data = data,
x = ~bucket, x = ~bucket,
y = ~count, y = ~count,
color = ~label color = ~source
) |> ) |>
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" barmode = "stack",
legend = list(title = list(text = "<b>Source of term</b>"))
) )
plotly::save_image(fig, image_path, width = 1200, height = 800) plotly::save_image(fig, image_path, width = 1200, height = 800)