genekitr (version 1.2.8)

plotEnrich: Plot for gene enrichment analysis of ORA method

Description

Over-representation analysis (ORA) is a simple method for objectively deciding whether a set of variables of known or suspected biological relevance, such as a gene set or pathway, is more prevalent in a set of variables of interest than we expect by chance.

Usage

plotEnrich(
  enrich_df,
  fold_change = NULL,
  plot_type = c("bar", "wego", "dot", "bubble", "lollipop", "geneheat", "genechord",
    "network", "gomap", "goheat", "gotangram", "wordcloud", "upset"),
  term_metric = c("FoldEnrich", "GeneRatio", "Count", "RichFactor"),
  stats_metric = c("p.adjust", "pvalue", "qvalue"),
  sim_method = c("Resnik", "Lin", "Rel", "Jiang", "Wang", "JC"),
  up_color = "#E31A1C",
  down_color = "#1F78B4",
  show_gene = "all",
  xlim_left = 0,
  xlim_right = NA,
  wrap_length = NULL,
  org = NULL,
  ont = NULL,
  scale_ratio,
  layout,
  n_term,
  ...
)

Value

A ggplot object

Arguments

enrich_df

Enrichment analysis `data.frame` result.

fold_change

Fold change or logFC values with gene IDs as names. Used in "heat" and "chord" plot.

plot_type

Choose from "bar", "wego","bubble","dot", "lollipop","geneheat", "genechord", "network","gomap","goheat","gotangram","wordcloud","upset".

term_metric

Pathway term metric from one of 'GeneRatio','Count','FoldEnrich' and 'RichFactor'.

stats_metric

Statistic metric from one of "pvalue", "p.adjust", "qvalue".

sim_method

Method of calculating the similarity between nodes, one of one of "Resnik", "Lin", "Rel", "Jiang" , "Wang" or "JC" (Jaccard’s similarity index). Only "JC" supports KEGG data. Used in "map","goheat","gotangram","wordcloud".

up_color

Color of higher statistical power (e.g. Pvalue 0.01) or higher logFC, default is "red".

down_color

Color of lower statistical power (e.g. Pvalue 1) or lower logFC, default is "blue".

show_gene

Select genes to show. Default is "all". Used in "heat" and "chord" plot.

xlim_left

X-axis left limit, default is 0.

xlim_right

X-axis right limit, default is NA.

wrap_length

Numeric, wrap text if longer than this length. Default is NULL.

org

Organism name from `biocOrg_name`.

ont

One of "BP", "MF", and "CC".

scale_ratio

Numeric, scale of node and line size.

layout

Grapgh layout in "map" plot, e,g, "circle", "dh", "drl", "fr","graphopt", "grid", "lgl", "kk", "mds", "nicely" (default),"randomly", "star".

n_term

Number of terms (used in WEGO plot)

...

other arguments from `plot_theme` function

Examples

# \donttest{
## example data
## More examples please refer to https://www.genekitr.fun/plot-ora-1.html
library(ggplot2)
data(geneList, package = "genekitr")
id <- names(geneList)[abs(geneList) > 1.5]
logfc <- geneList[id]

gs <- geneset::getGO(org = "human",ont = "bp",data_dir = tempdir())
ego <- genORA(id, geneset = gs)
ego <- ego[1:10, ]

## example plots
plotEnrich(ego, plot_type = "dot")

#plotEnrich(ego, plot_type = "bubble", scale_ratio = 0.4)

#plotEnrich(ego, plot_type = "bar")

# }