xEnrichTreemap: Function to visualise enrichment results using a treemap

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

Function to visualise enrichment results using a treemap

Description

xEnrichTreemap is supposed to visualise enrichment results using a treemap. The area is proportional to odds ratio, colored by the significance level. It returns an object of class "ggplot".

Usage

xEnrichTreemap(
eTerm,
top_num = 10,
FDR.cutoff = 0.05,
CI.one = T,
colormap = "spectral.top",
ncolors = 64,
zlim = NULL,
barwidth = NULL,
barheight = 0.5,
wrap.width = NULL,
font.family = "sans",
drop = F,
details = c("name", "name_FDR", "name_FDR_members"),
caption = T,
treemap.grow = F,
treemap.reflow = F,
treemap.place = "topleft",
treemap.color = "black",
treemap.fontface = "bold.italic",
treemap.min.size = 4,
area = c("adjp", "or"),
area.fill = c("or", "adjp", "zscore")
)

Arguments

eTerm	an object of class "eTerm" or "ls_eTerm". Alterntively, it can be a data frame having these columns (named as 'group','ontology','name','zscore','adjp','or','CIl','CIu','nOverlap','members_Overlap') in which 'name','zscore','adjp','or','CIl','CIu' are required
top_num	the number of the top terms (sorted according to OR). If it is 'auto', only the significant terms (see below FDR.cutoff) will be displayed
FDR.cutoff	FDR cutoff used to declare the significant terms. By default, it is set to 0.05
CI.one	logical to indicate whether to allow the inclusion of one in CI. By default, it is TURE (allowed)
colormap	short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
ncolors	the number of colors specified over the colormap
zlim	the minimum and maximum z values for which colors should be plotted, defaulting to the range of the -log10(FDR)
barwidth	the width of the colorbar. Default value is 'legend.key.width' or 'legend.key.size' in 'theme' or theme
barheight	the height of the colorbar. Default value is 'legend.key.height' or 'legend.key.size' in 'theme' or theme
wrap.width	a positive integer specifying wrap width of name
font.family	the font family for texts
drop	logical to indicate whether all factor levels not used in the data will automatically be dropped. If FALSE (by default), all factor levels will be shown, regardless of whether or not they appear in the data
details	how to label. It can be one of 'name', 'name_FDR' (FDR/OR also appended to the name), and 'name_FDR_members' (FDR/OR plus members appended to the name; in this case, treemap.grow and treemap.reflow is forced to be true)
caption	logical to indicate whether the caption is shown on the bottom-right
treemap.grow	logical to indicate whether text will be grown as well as shrunk to fill the box
treemap.reflow	logical to indicate whether text will be reflowed (wrapped) to better fit the box
treemap.place	where inside the box to place the text. Default is "centre"; other options are "bottom", "top", "topleft", "topright", etc
treemap.color	the color of the text
treemap.fontface	the fontface of the text
treemap.min.size	the minimum font size, in points. If provided, text that would need to be shrunk below this size to fit the box will not be drawn. Defaults to 4 pt
area	which statistics will be used for the area. It can be "adjp" for adjusted p value (FDR) and "or" for odds ratio
area.fill	which statistics will be used for the area fill color. It can be "or" for the odds ratio, "adjp" for adjusted p value (FDR) and "zscore" for enrichment z-score

Value

an object of class "ggplot"

Note

none

See Also

xEnricherGenes, xEnricherSNPs, xEnrichViewer

Examples

## Not run: 
# Load the library
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"
library(treemapify)

# provide the input Genes of interest (eg 100 randomly chosen human genes)
## load human genes
org.Hs.eg <- xRDataLoader(RData='org.Hs.eg',
RData.location=RData.location)
set.seed(825)
data <- as.character(sample(org.Hs.eg$gene_info$Symbol, 100))
data

# optionally, provide the test background (if not provided, all human genes)
#background <- as.character(org.Hs.eg$gene_info$Symbol)

# 1) Gene-based enrichment analysis using REACTOME pathways
# perform enrichment analysis
eTerm <- xEnricherGenes(data, ontology="REACTOME",
RData.location=RData.location)
## forest plot of enrichment results
gp <- xEnrichTreemap(eTerm, top_num=20, FDR.cutoff=0.05,
treemap.reflow=F, treemap.place="topleft")

# 2) Gene-based enrichment analysis using ontologies (REACTOME and GOMF)
# perform enrichment analysis
ls_eTerm <- xEnricherGenesAdv(data, ontologies=c("REACTOME","GOMF"),
RData.location=RData.location)
## forest plot of enrichment results
gp <- xEnrichTreemap(ls_eTerm, FDR.cutoff=0.1)

## End(Not run)

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