plotRunningScore {PEIMAN2}

Plot running score plot for the results of psea

Description

This function takes results generated by runPSEA. It plots running enrichment score of ranked protein for each PTM.

Usage

plotRunningScore(
  x,
  nplot = length(x$psea.result),
  type = "l",
  lty = 1,
  lwd = 3,
  cex = 1.2,
  cex.axis = 1.2,
  cex.lab = 1.1,
  col = "blue"
)

Arguments

x

A list of 6 generated by runPSEA function.

nplot

An integer that defines the number of running score plots to show. Default value is the number of enriched PTMs in x.

type

Type of line used in the plot.

lty

A list of 6 generated by runPSEA function.

lwd

line width

cex

Specify the size of the title text

cex.axis

Specify the size of the tick label

cex.lab

Specify the size of the axis label text

col

Color of running enrichment score line

Value

Plot

Examples

# We recommend at least nperm = 1000.
# The number of permutations was reduced to 10
# to accommodate CRAN policy on examples (run time <= 5 seconds).
psea_res <- runPSEA(protein = exmplData2, os.name = 'Rattus norvegicus (Rat)', nperm = 10)
plotRunningScore(x = psea_res)