View source: R/do_GroupedGOTermPlot.R
do_GroupedGOTermPlot | R Documentation |
Compute an overview of the GO terms associated with the input list of genes.
do_GroupedGOTermPlot(
genes,
org.db,
levels.use = NULL,
GO_ontology = "BP",
min.overlap = 3,
flip = TRUE,
colors.use = c(Present = "#1e3d59", Absent = "#bccbcd"),
legend.position = "bottom",
reverse.levels = TRUE,
axis.text.x.angle = 45,
font.size = 10,
font.type = "sans",
plot.title = paste0("GO | ", GO_ontology),
plot.subtitle = NULL,
plot.caption = NULL,
verbose = FALSE,
return_matrices = FALSE,
grid.color = "white",
border.color = "black",
plot.title.face = "bold",
plot.subtitle.face = "plain",
plot.caption.face = "italic",
axis.title.face = "bold",
axis.text.face = "plain",
legend.title.face = "bold",
legend.text.face = "plain"
)
genes |
|
org.db |
|
levels.use |
|
GO_ontology |
|
min.overlap |
|
flip |
|
colors.use |
|
legend.position |
|
reverse.levels |
|
axis.text.x.angle |
|
font.size |
|
font.type |
|
plot.title, plot.subtitle, plot.caption |
|
verbose |
|
return_matrices |
|
grid.color |
|
border.color |
|
plot.title.face, plot.subtitle.face, plot.caption.face, axis.title.face, axis.text.face, legend.title.face, legend.text.face |
|
A list containing all the matrices for the respective GO levels and all the individual and combined heatmaps.
# Check Suggests.
value <- SCpubr:::check_suggests(function_name = "do_GroupedGOTermPlot", passive = TRUE)
if (isTRUE(value)){
# Consult the full documentation in https://enblacar.github.io/SCpubr-book/
# Need to load this library or equivalent.
suppressMessages(library("org.Hs.eg.db"))
# Define list of genes to query.
genes.use <- c("CCR7", "CD14", "LYZ",
"S100A4", "MS4A1",
"MS4A7", "GNLY", "NKG7", "FCER1A",
"CST3", "PPBP")
# Compute the grouped GO terms.
out <- SCpubr::do_GroupedGOTermPlot(genes = genes.use,
org.db = org.Hs.eg.db)
} else if (base::isFALSE(value)){
message("This function can not be used without its suggested packages.")
message("Check out which ones are needed using `SCpubr::state_dependencies()`.")
}
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