plotPPiProfiles: Plot thermal profile of protein pairs

In Rtpca: Thermal proximity co-aggregation with R

Description

Plot thermal profile of protein pairs

Usage

plotPPiProfiles(tpcaObj, pair, splinesDf = 4)

Arguments

tpcaObj	a tpcaObj after having performed a differential analysis, see runDiffTPCA
pair	character vector of one or more protein names
splinesDf	numeric, degree of freedom of the spline fit to the melting curves

Value

ggplot displaying the thermal profile of a protein pair across conditions

Examples

library(Biobase)

set.seed(12)
m1 <- matrix(rnorm(50), ncol = 10)
m2 <- matrix(rnorm(50), ncol = 10)

rownames(m1) <- letters[1:5]
rownames(m2) <- letters[1:5]

colnames(m1) <- paste("fc", 1:10, sep = "_")
colnames(m2) <- paste("fc", 1:10, sep = "_")

pheno <- data.frame(
    temperature = seq(37, 67, length.out = 10))
rownames(pheno) <- paste("fc", 1:10, sep = "_")

eset1 <- ExpressionSet(
    assayData = m1,
    phenoData = AnnotatedDataFrame(pheno)
)

eset2 <- ExpressionSet(
    assayData = m2,
    phenoData = AnnotatedDataFrame(pheno)
)

tpcaObj <- new("tpcaResult",
               ObjList = list(eset1),

ContrastList = list(eset2),
                CtrlCondName = "control",
                ContrastCondName = "treatment")

plotPPiProfiles(tpcaObj, pair = c("b", "d"))

Rtpca documentation built on Nov. 8, 2020, 7:44 p.m.