XGR (version 1.1.7)

xEnrichBarplot: 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"

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()
# }
# 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()
# }