TOmicsVis (version 2.0.0)

kegg_enrich_dot: KEGG enrichment analysis and dot plot (None/Exist Reference Genome).

Description

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

Usage

kegg_enrich_dot(
  kegg_anno,
  degs_list,
  padjust_method = "fdr",
  pvalue_cutoff = 0.05,
  qvalue_cutoff = 0.05,
  sign_by = "p.adjust",
  category_num = 30,
  font_size = 12,
  low_color = "#ff0000aa",
  high_color = "#008800aa",
  ggTheme = "theme_light"
)

Value

Plot: KEGG enrichment analysis and dot 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.

sign_by

Character: significant by. Default: "p.adjust", options: "pvalue", "p.adjust", "qvalue".

category_num

Numeric: categories number to display. Default: 30, min: 1, max: NULL.

font_size

Numeric: category font size. Default: 12.

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).

ggTheme

Character: ggplot2 themes. Default: "theme_light", options: "theme_default", "theme_bw", "theme_gray", "theme_light", "theme_linedraw", "theme_dark", "theme_minimal", "theme_classic", "theme_void"

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_dot(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1])

# 4. Set padjust_method = "BH"
kegg_enrich_dot(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1], padjust_method = "BH")

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

# 6. Set ggTheme = "theme_bw"
kegg_enrich_dot(gene_go_kegg[,c(1,5)], gene_go_kegg[100:200,1], ggTheme = "theme_bw")