get_go_emap_plot | R Documentation |
Perform gene ontology analysis and visualization for DE genesets in one go.
get_go_emap_plot(
x,
org_db = org.Hs.eg.db::org.Hs.eg.db,
universe = NULL,
ont_type = "BP",
p_adj_method = "BH",
pval_cutoff = 0.05,
qval_cutoff = 0.05,
simplify = TRUE,
min_geneset_size = 10,
max_geneset_size = 500,
go_similarity_cutoff = 0.8,
show_n_terms = 30,
color_terms_by = "p.adjust"
)
x |
an object of class 'parcutils' or 'parcutils_ir'. |
org_db |
an object of the class class OrgDB, default |
universe |
a character vector of genes, default NULL, to be used as background genes for GO enrichment analysis. Currently supports only ENSEMBL gene id - e.g. ENSMUSG00000030787. When set to NULL all genes from x will be used as background genes. |
ont_type |
a character string, default |
p_adj_method |
a character string, default |
pval_cutoff |
a numeric, default |
qval_cutoff |
a numeric, default |
min_geneset_size |
a numeric, default |
max_geneset_size |
a numeric, default |
go_similarity_cutoff |
a numeric value, default |
show_n_terms |
a numeric, default |
color_terms_by |
a character string, default |
An EMAP plot.
## Not run:
count_file <- system.file("extdata","toy_counts.txt" , package = "parcutils")
count_data <- readr::read_delim(count_file, delim = "\t", show_col_types = FALSE)
sample_info <- count_data %>% colnames() %>% .[-1] %>%
tibble::tibble(samples = . , groups = rep(c("control" ,"treatment1" , "treatment2"), each = 3) )
res <- parcutils::run_deseq_analysis(counts = count_data %>% dplyr::mutate(gene_id = stringr::str_replace(gene_id, ":.*","")),
sample_info = sample_info,
column_geneid = "gene_id" ,
group_numerator = c("treatment1", "treatment2") ,
group_denominator = c("control"))
go_out <- get_go_emap_plot(res)
# display plot
go_out$go_emap_plots
# display table
go_out$go_enrichment_output %>% tibble::as_tibble()
## End(Not run)
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