View source: R/do_FunctionalAnnotationPlot.R
do_FunctionalAnnotationPlot | R Documentation |
Compute functional annotation plots using GO or KEGG ontologies
do_FunctionalAnnotationPlot(
genes,
org.db,
organism = "hsa",
database = "GO",
GO_ontology = "BP",
min.overlap = NULL,
p.adjust.cutoff = 0.05,
pAdjustMethod = "BH",
minGSSize = 10,
maxGSSize = 500,
font.size = 10,
font.type = "sans",
axis.text.x.angle = 45,
xlab = NULL,
ylab = NULL,
plot.title = NULL,
plot.subtitle = NULL,
plot.caption = NULL,
legend.type = "colorbar",
legend.position = "bottom",
legend.framewidth = 0.5,
legend.tickwidth = 0.5,
legend.length = 10,
legend.width = 1,
legend.framecolor = "grey50",
legend.tickcolor = "white",
number.breaks = 5,
return_matrix = 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 |
|
organism |
|
database |
|
GO_ontology |
|
min.overlap |
|
p.adjust.cutoff |
|
pAdjustMethod |
|
minGSSize |
|
maxGSSize |
|
font.size |
|
font.type |
|
axis.text.x.angle |
|
xlab, ylab |
|
plot.title, plot.subtitle, plot.caption |
|
legend.type |
|
legend.position |
|
legend.framewidth, legend.tickwidth |
|
legend.length, legend.width |
|
legend.framecolor |
|
legend.tickcolor |
|
number.breaks |
|
return_matrix |
|
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 a heatmap of the presence/absence of the genes in the enriched term, as well as a bar plot, dot plot and tree plot of the enriched terms.
# Check Suggests.
value <- SCpubr:::check_suggests(function_name = "do_FunctionalAnnotationPlot", 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_FunctionalAnnotationPlot(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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