xEnrichBarplot: Function to visualise enrichment results using a barplot

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Function to visualise enrichment results using a barplot

Description

xEnrichBarplot is supposed to visualise enrichment results using a barplot. It returns an object of class "ggplot".

Usage

xEnrichBarplot(
eTerm,
top_num = 10,
displayBy = c("fc", "adjp", "fdr", "zscore", "pvalue"),
FDR.cutoff = 0.05,
bar.label = TRUE,
bar.label.size = 3,
bar.color = "lightyellow-orange",
bar.width = 0.8,
wrap.width = NULL,
font.family = "sans",
signature = TRUE
)

Arguments

eTerm	an object of class "eTerm"
top_num	the number of the top terms (sorted according to FDR or adjusted p-values). If it is 'auto', only the significant terms (see below FDR.cutoff) will be displayed
displayBy	which statistics will be used for displaying. It can be "fc" for enrichment fold change (by default), "adjp" or "fdr" for adjusted p value (or FDR), "pvalue" for p value, "zscore" for enrichment z-score
FDR.cutoff	FDR cutoff used to declare the significant terms. By default, it is set to 0.05. This option only works when setting top_num (see above) is 'auto'
bar.label	logical to indicate whether to label each bar with FDR. By default, it sets to true for bar labelling
bar.label.size	an integer specifying the bar labelling text size. By default, it sets to 3
bar.color	either NULL or fill color names ('lightyellow-orange' by default)
bar.width	bar width. By default, 80 data
wrap.width	a positive integer specifying wrap width of name
font.family	the font family for texts
signature	logical to indicate whether the signature is assigned to the plot caption. By default, it sets TRUE showing which function is used to draw this graph

Value

an object of class "ggplot"

Note

none

See Also

xEnricherGenes, xEnricherSNPs, xEnrichViewer

Examples

## Not run: 
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"

# 1) load eQTL mapping results: cis-eQTLs significantly induced by IFN
cis <- xRDataLoader(RData.customised='JKscience_TS2A',
RData.location=RData.location)
ind <- which(cis$IFN_t > 0 & cis$IFN_fdr < 0.05)
df_cis <- cis[ind, c('variant','Symbol','IFN_t','IFN_fdr')]
data <- df_cis$variant

# 2) Enrichment analysis using Experimental Factor Ontology (EFO)
# Considering LD SNPs and respecting ontology tree
eTerm <- xEnricherSNPs(data, ontology="EF", include.LD="EUR",
LD.r2=0.8, ontology.algorithm="lea", RData.location=RData.location)

# 3) Barplot of enrichment results
bp <- xEnrichBarplot(eTerm, top_num="auto", displayBy="fc")
#pdf(file="enrichment_barplot.pdf", height=6, width=12, compress=TRUE)
print(bp)
#dev.off()

## End(Not run)

# 4) use font family (Arial)
## Not run: 
BiocManager::install("extrafont")
library(extrafont)
font_import()
fonttable()
## creating PDF files with fonts
library(extrafont)
loadfonts()
bp <- xEnrichBarplot(eTerm, top_num="auto", displayBy="fc",
font.family="Arial Black")
pdf(file="enrichment_barplot_fonts.pdf", height=6, width=12,
family="Arial Black")
print(bp)
dev.off()

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.