xGSEAdotplot: Function to visualise GSEA results using dot plot

Description Usage Arguments Value Note See Also Examples

View source: R/xGSEAdotplot.r

Description

xGSEAdotplot is supposed to visualise GSEA results using dot plot. It returns an object of class "ggplot" or a list of "ggplot" objects.

Usage

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xGSEAdotplot(
eGSEA,
top = 1,
colormap = "lightblue-darkblue",
zlim = NULL,
ncolors = 64,
xlab = NULL,
title = c("name", "setID", "none"),
subtitle = c("leading", "enrichment", "both", "none"),
clab = "Pi rating",
x.scale = c("normal", "sqrt", "log"),
peak = TRUE,
peak.color = "red",
leading = FALSE,
leading.size = 2,
leading.color = "black",
leading.alpha = 0.6,
leading.padding = 0.2,
leading.arrow = 0.01,
leading.force = 0.01,
leading.query = NULL,
leading.query.only = FALSE,
leading.edge.only = FALSE,
compact = FALSE,
font.family = "sans",
signature = TRUE,
...
)

Arguments

eGSEA

an object of class "eGSEA"

top

the number of the top enrichments to be visualised. Alternatively, the gene set names can be queried

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

zlim

the minimum and maximum z values for which colors should be plotted

ncolors

the number of colors specified over the colormap

xlab

the label for x-axis. If NULL, it is 'Target ranks'

title

the title. If NULL, it is term name followed by the number of its annotations

subtitle

the subtitle. It can be used to show 'leading' info, 'enrichment' info or 'both'

clab

the label for colorbar. By default, it is '5-star ratings'

x.scale

how to transform the x scale. It can be "normal" for no transformation, "sqrt" for square root transformation, and "log" for log-based transformation

peak

logical to indicate whether the peak location is shown

peak.color

the peak color

leading

logical to indicate whether the leading targets are texted. Alterntively, leading can be numeric to restict the top targets displayed

leading.size

the size of leading targets' texts. It only works when the parameter 'leading' is enabled

leading.color

the label color of leading targets' texts

leading.alpha

the 0-1 value specifying transparency of leading targets' texts

leading.padding

the padding around the leading targets' texts

leading.arrow

the arrow pointing to the leading targets

leading.force

the repelling force between leading targets' texts

leading.query

which genes in query will be labelled. By default, it sets to NULL meaning all genes will be displayed. If labels in query can not be found, then all will be displayed

leading.query.only

logical to indicate whether only genes in query will be displayed. By default, it sets to FALSE. It only works when labels in query are enabled/found

leading.edge.only

logical to indicate whether only the leading edge will be shown. By default, it sets to FALSE

compact

logical to indicate whether the compact/void theme is used. If TRUE, axes and legend info will be hidden

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

...

additional paramters associated with ggrepel::geom_text_repel. If queried, it has high priority (eg, color='darkred',size=2,alpha=0.6,fontface='bold')

Value

an object of class "ggplot" or a list of "ggplot" objects.

Note

none

See Also

xGSEAdotplot

Examples

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RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
gp <- xGSEAdotplot(eGSEA, top=1)
#gp <- xGSEAdotplot(eGSEA, top=1, peak=FALSE, compact=TRUE, signature=FALSE)
gp

ls_gp <- xGSEAdotplot(eGSEA, top=1:4, signature=FALSE)
library(gridExtra)
grid.arrange(grobs=ls_gp, ncol=2)

## End(Not run)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.