xGSEAdotplot: Function to visualise GSEA results using dot plot

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

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

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

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.