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Updated vignette.
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GriffyGe committed Dec 7, 2024
1 parent ca0483f commit 60edfcc
Showing 2 changed files with 7 additions and 6 deletions.
13 changes: 7 additions & 6 deletions vignettes/mapa.Rmd
Original file line number Diff line number Diff line change
@@ -91,7 +91,6 @@ enriched_modules <-
sim.cutoff.kegg = 0.5,
sim.cutoff.reactome = 0.5,
measure.method.go = "Sim_XGraSM_2013",
control.method.go = list(),
measure.method.kegg = "jaccard",
measure.method.reactome = "jaccard",
path = "result",
@@ -146,9 +145,11 @@ plot_pathway_bar(
line_type = "straight"
)
# plot_pathway_bar(object = enriched_functional_module,
# top_n = 20,
# level = "module")
plot_pathway_bar(object = enriched_functional_module,
top_n = 20,
level = "module",
x_axis_name = "RichFactor",
line_type = "straight")
plot_pathway_bar(object = enriched_functional_module,
top_n = 20,
@@ -203,8 +204,8 @@ plot_similarity_network(
object = enriched_functional_module,
level = "module",
database = "go",
degree_cutoff = 10,
module_id = "go_Module_10",
degree_cutoff = 0,
module_id = "go_Module_2",
text_all = TRUE
)
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