| xEnrichBarplot | R Documentation |
xEnrichBarplot is supposed to visualise enrichment results using
a barplot. It returns an object of class "ggplot".
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
)
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 |
an object of class "ggplot"
none
xEnricherGenes, xEnricherSNPs,
xEnrichViewer
## 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)