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Plot protein domains from Ensembl

Source: R/plot_gene_domains.R
plot_gene_domains.Rd

Plot protein domains from Ensembl.

Usage

plot_gene_domains(
  gene_name = NULL,
  species = "hsapiens",
  transcript_id = NULL,
  transcript_choice = "longest",
  palette = "Set 2",
  legend_ncol = 2,
  return_data = FALSE
)

Arguments

gene_name

Official gene symbol. ("TP53").

species

Species in BioMart format. ("hsapiens", "mmusculus").

transcript_id

Ensembl transcript ID. ("ENST00000269305").

transcript_choice

Transcript choice. ("longest", "canonical").

palette

Color palette. ("Set 2", "Set 2", "Set 3", "Warm", "Cold", "Dynamic", "Viridis", "Plasma", "Inferno", "Rocket", "Mako").

legend_ncol

Legend columns per row. (2).

return_data

Plot and data. (TRUE).

Value

Plot of protein domains.

Author

benben-miao

Examples

# Plot TP53 domian
res <- plot_gene_domains(
  gene_name = "TP53",
  species = "hsapiens",
  transcript_id = NULL,
  transcript_choice = "longest",
  palette = "Set 2",
  legend_ncol = 2,
  return_data = TRUE)

res$plot

head(res$domain_data)
#>                         domain start end   type
#> 1 p53 tumour suppressor family   116 142 domain
#> 2 p53 tumour suppressor family   158 179 domain
#> 3 p53 tumour suppressor family   213 234 domain
#> 4 p53 tumour suppressor family   236 258 domain
#> 5 p53 tumour suppressor family   264 286 domain
#> 6 p53 tumour suppressor family   326 350 domain