XGR (version 1.1.5)

xEnrichMatrix: Function to compare enrichment results using matrix plots

Description

xEnrichMatrix is supposed to compare enrichment results using matrix plots.

Usage

xEnrichMatrix(list_eTerm, method = c("ggplot2", "circle", "square",
"color", "pie"), displayBy = c("zscore", "fc", "adjp", "pvalue"),
FDR.cutoff = 0.05, wrap.width = NULL, sharings = NULL,
reorder = c("row", "none", "col", "both"), colormap = "jet",
ncolors = 20, zlim = NULL, slim = NULL,
legend.direction = c("horizontal", "vertical"), title = NULL,
flip = FALSE, y.rotate = 45, shape = 19, font.family = "sans",
...)

Arguments

list_eTerm

a list of "eTerm" objects, or a data frame (with at least 3 columns "group", "name" and "adjp")

method

which method will be used for plotting. It can be "circle" (by default), "square", "color" and "pie"

displayBy

which statistics will be used for comparison. It can be "fc" for enrichment fold change (by default), "adjp" 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

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

reorder

how to reorder rows and columns. It can be "none" for no reordering, "row" for reordering rows according to number of sharings (by default), "col" for reordering columns, and "both" for reordering rows and columns

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 finite values of displayed matrix

slim

the minimum and maximum displaying values for which sizes should be plotted

legend.direction

the legend guide direction. It can be "horizontal" (useful for many groups with lengthy labelling), "vertical"

title

the title of the plot. By default, it is NULL

flip

logical to indicate whether to flip the coordiate. By default, it sets to false

y.rotate

the angle to rotate the y tick labelings. By default, it is 45

shape

the number specifying the shape. By default, it is 19

font.family

the font family for texts

...

additional graphic parameters for corrplot::corrplot

Value

If the method is 'ggplot2', it returns a ggplot object. Otherwise, it is a data frame

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/"
xEnrichMatrix(list_eTerm, method="circle", displayBy="adjp",
FDR.cutoff=0.05, wrap.width=50, sharings=NULL, reorder="row",
colormap="black-yellow-red", ncolors=16, zlim=c(0,8), cl.pos="b",
cl.ratio=0.1, cl.align.text="c", tl.col="black", tl.cex=0.7, tl.srt=90,
title=paste0(ontology,": log10(FDR)"))
xEnrichMatrix(list_eTerm, method="pie", displayBy="adjp",
FDR.cutoff=0.05, wrap.width=50, sharings=NULL, reorder="row",
colormap="grey-grey", ncolors=1, zlim=c(0,8), cl.pos="n", cl.ratio=0.1,
cl.align.text="c", tl.col="black", tl.cex=0.7, tl.srt=90,
title=paste0(ontology,": log10(FDR)"))
gp <- xEnrichMatrix(list_eTerm, method="ggplot2", displayBy="zscore",
FDR.cutoff=0.05, wrap.width=40, sharings=NULL, reorder="row",
colormap="yellow-red", flip=T, y.rotate=45, font.family=font.family)
# }