TOmicsVis (version 2.0.0)

kegg_enrich_net: KEGG enrichment analysis and net plot (None/Exist Reference Genome).

Description

KEGG enrichment analysis and net plot (None/Exist Reference Genome).

Usage

kegg_enrich_net(
  kegg_anno,
  degs_list,
  padjust_method = "fdr",
  pvalue_cutoff = 0.05,
  qvalue_cutoff = 0.05,
  category_num = 20,
  net_layout = "circle",
  net_circular = TRUE,
  low_color = "#ff0000aa",
  high_color = "#008800aa"
)

Value

Plot: KEGG enrichment analysis and net plot (None/Exist Reference Genome).

Arguments

kegg_anno

Dataframe: GO and KEGG annotation of background genes (1st-col: Genes, 2nd-col: biological_process, 3rd-col: cellular_component, 4th-col: molecular_function, 5th-col: kegg_pathway).

degs_list

Dataframe: degs list.

padjust_method

Character: P-value adjust to Q-value. Default: "fdr" (false discovery rate), options: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

pvalue_cutoff

Numeric: P-value cutoff. Recommend: small than 0.05.

qvalue_cutoff

Numeric: Q-value cutoff. Recommend: small than 0.05.

category_num

Numeric: categories number to display. Default: 20, min: 1, max: NULL.

net_layout

Character: network layout. Default: "circle", options: 'star', 'circle', 'gem', 'dh', 'graphopt', 'grid', 'mds', 'randomly', 'fr', 'kk', 'drl' or 'lgl'.

net_circular

Logical: network circular. Default: TRUE, options: TRUE, FALSE.

low_color

Character: low value (p-value or q-value) color (color name or hex value).

high_color

Character: high value (p-value or q-value) color (color name or hex value).

Author

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(gene_go_kegg)
head(gene_go_kegg)

# 3. Default parameters
kegg_enrich_net(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1])

# 4. Set category_num = 10
kegg_enrich_net(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1], category_num = 10)