Plot the N-cycling pathway and genes

plot_N_cycle(
  my_N_genes = NULL,
  just_diff = FALSE,
  path_col = NULL,
  type_col = c(up = "red", down = "blue", none = NA),
  fill_alpha = 0.5,
  arrow_size = 0.1,
  line_width = 1,
  title = "Nitrogen cycling",
  legend.position = c(0.85, 0.15)
)

Arguments

my_N_genes: dataframe, "Gene_families","type" should in colnames of my_N_genes
just_diff: logical, just plot the different genes?
path_col: colors of pathways
type_col: colors of types
fill_alpha: alpha, default 0.5
arrow_size: arrow_size, default 0.1
line_width: line_width, default 1
title: title, default "Nitrogen cycling"
legend.position: default c(0.85,0.15)

Value

ggplot

Examples

N_data <- load_N_data()
#> Joining with `by = join_by(Pathway2)`
my_N_genes <- data.frame(
  `Gene_families` = sample(N_data$N_genes$Gene_families, 10, replace = FALSE),
  change = rnorm(10), check.names = FALSE
)
my_N_genes <- dplyr::mutate(my_N_genes,
  type = ifelse(change > 0, "up", ifelse(change < 0, "down", "none"))
)
plot_N_cycle(my_N_genes, just_diff = FALSE, fill_alpha = 0.2)
#> Joining with `by = join_by(Pathway2)`
#> recommend ggsave(width = 14,height = 10)
#> Joining with `by = join_by(Gene_families)`

# ggsave(filename = "test.pdf", width = 14, height = 10)