plotEnrichment: Plot the enrichment of domains that are likely to be...

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

Description

Plot the enrichment of domains that are likely to be mediating interactions in domain annotated by ELM as mediating linear motif mediated interactions

Usage

plotEnrichment(..., runningTestEnrichmentlist = list(),
  random_domains = NULL, domains_known_mapped, type = "count",
  plot_type = "l", plot_name = "", plot_args = NULL,
  legend_args = NULL, leg_pos_x = NULL, show_known_domains = F,
  plot_total_domains_found = F)

Arguments

...	objects (matrix) the output of runningTestEnrichment
random_domains	the result of comparing random domain-protein pairs (by random_domains function), can be null
domains_known_mapped	domains from ELM mapped to InterProID
type	what to plot: "pval"- Fisher test p-val (in out set vs in ELM), "odds_ratio" - Fisher test odds ratio, "count" of domains in our set that are in ELM
plot_type	r-base plot type default is "l"
plot_name	to be passed to plot(main = *)
plot_args	other arguments to plot: to be passed as vector of characters, such as c("cex = 1.2", "family = \"Helvetica\"")
legend_args	other arguments to legend: to be passed as vector of characters, such as c("cex = 1.2")
list	list of object (alternative way to pass the output of runningTestEnrichment)

Value

plot

Author(s)

Vitalii Kleshchevnikov

vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.