XGR (version 1.1.7)

xEnrichCompare: Function to compare enrichment results using side-by-side barplots

Description

xEnrichCompare is supposed to compare enrichment results using side-by-side barplots. It returns an object of class "ggplot".

Usage

xEnrichCompare(
list_eTerm,
displayBy = c("fc", "adjp", "fdr", "zscore", "pvalue"),
FDR.cutoff = 0.05,
bar.label = TRUE,
bar.label.size = 2.5,
wrap.width = NULL,
sharings = NULL,
font.family = "sans",
facet = TRUE,
signature = TRUE
)

Arguments

list_eTerm

a list of "eTerm" objects

displayBy

which statistics will be used for comparison. 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

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

wrap.width

a positive integer specifying wrap width of name

sharings

a numeric vector specifying whether only shared terms will be displayed. For example, when comparing three groups of enrichment results, it can be set into c(2,3) to display only shared terms by any two or all three. By default, it is NULL meaning no such restriction

font.family

the font family for texts

facet

logical to indicate whether to facet/wrap a 1d of panels into 2d. By default, it sets TRUE

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", but appended with a 'g' (an igraph object to represent DAG after being unionised)

See Also

xEnricherGenes, xEnricherSNPs, xEnrichDAGplotAdv

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)
# 2a) Without considering LD SNPs and without respecting ontology tree
eTerm_noLD_noTree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD=NA, ontology.algorithm="none",
RData.location=RData.location)
# 2b) Without considering LD SNPs but respecting ontology tree
eTerm_noLD_Tree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD=NA, ontology.algorithm="lea", RData.location=RData.location)
# 2c) Considering LD SNPs but without respecting ontology tree
eTerm_LD_noTree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD="EUR", LD.r2=0.8, ontology.algorithm="none",
RData.location=RData.location)
# 2d) Considering LD SNPs and respecting ontology tree
eTerm_LD_Tree <- xEnricherSNPs(data, ontology="EF_disease",
include.LD="EUR", LD.r2=0.8, ontology.algorithm="lea",
RData.location=RData.location)

# 3) Compare enrichment results
list_eTerm <- list(eTerm_noLD_noTree, eTerm_noLD_Tree, eTerm_LD_noTree,
eTerm_LD_Tree)
names(list_eTerm) <- c('LD(-) & Tree(-)','LD(-) & Tree(+)','LD(+) &
Tree(-)','LD(+) & Tree(+)')
## side-by-side comparisons 
bp <- xEnrichCompare(list_eTerm, displayBy="fc")
#pdf(file="enrichment_compared.pdf", height=6, width=12, compress=TRUE)
print(bp)
#dev.off()
## modify y axis text
bp + theme(axis.text.y=element_text(size=10,color="black"))
## modify x axis title
bp + theme(axis.title.x=element_text(color="black"))
## modify fill colors
bp + scale_fill_manual(values=c("black","#888888"))
## show legend title but hide strip
bp + theme(legend.position="right", strip.text=element_blank())

# 4) DAGplot of comparative enrichment results in the context of ontology tree
xEnrichDAGplotAdv(bp, graph.node.attrs=list(fontsize=100))
# }