plot_element_cycle: Plot element cycle

In pctax: Professional Comprehensive Omics Data Analysis

Plot element cycle

Description

Plot element cycle

Usage

plot_element_cycle(
  cycle = "Nitrogen cycle",
  anno_df = NULL,
  only_anno = FALSE,
  cell_fill = NA,
  cell_color = "orange",
  chemical_size = 7,
  chemical_bold = TRUE,
  chemical_color = "black",
  chemical_label = TRUE,
  reaction_width = 1,
  reaction_arrow_size = 4,
  reaction_arrow_closed = TRUE,
  gene_or_ko = "gene",
  gene_size = 3,
  gene_x_offset = 0.3,
  gene_y_offset = 0.15,
  gene_label = TRUE,
  gene_color = NULL,
  gene_bold = TRUE,
  gene_italic = TRUE,
  gene_label_fill = "white"
)

Arguments

cycle	one of c("Carbon cycle","Nitrogen cycle","Phosphorus cycle","Sulfur cycle","Iron cycle")
anno_df	anno_df, columns should contains Gene or KO and Group
only_anno	only show genes in anno_df?
cell_fill	cell fill color
cell_color	cell border color
chemical_size	chemical text size
chemical_bold	chemical text bold
chemical_color	chemical text color
chemical_label	chemical text in geom_label or geom_text?
reaction_width	reaction line width
reaction_arrow_size	reaction arrow size
reaction_arrow_closed	reaction arrow closed?
gene_or_ko	"gene" or "ko"
gene_size	gene text size
gene_x_offset	gene_x_offset
gene_y_offset	gene_y_offset
gene_label	gene text in geom_label or geom_text?
gene_color	gene text color
gene_bold	gene text blod?
gene_italic	gene text italic?
gene_label_fill	gene label fill color

Value

ggplot

Examples

if (requireNamespace("ggforce")) plot_element_cycle()

pctax documentation built on May 29, 2024, 10:03 a.m.