Rex volcano plots for differential analysis

Rex volcano plots for differential analysis

plotVolcano(diff_params, nrow = 5, quantity = "TRE")

Arguments

diff_params

An object of class RexDifferential

nrow

The number of rows in the facet (to seperate timepoints)

quantity

The quantity to plot either "TRE" or "ARE"

Value

Returns a ggplot object

Examples

require(RexMS)
require(dplyr)
require(ggplot2)

data("BRD4_apo")
data("BRD4_ibet")
BRD4_apo <- BRD4_apo %>% filter(End < 100)
BRD4_ibet <- BRD4_ibet %>% filter(End < 100)
numTimepoints <- length(unique(BRD4_apo$Exposure))
Timepoints <- unique(BRD4_apo$Exposure)
numPeptides <- length(unique(BRD4_apo$Sequence))

rex_test <- rex(HdxData = DataFrame(BRD4_ibet),
                numIter = 10,
                R = max(BRD4_ibet$End),
                numtimepoints = numTimepoints,
                timepoints = Timepoints,
                seed = 1L,
                tCoef = c(0, rep(1, 5)),
                BPPARAM = SerialParam())
#> Fold 1 ... Fold 2 ... Fold 3 ... Fold 4 ... Fold 5 ... 
#> 
  |                                                                            
  |                                                                      |   0%
#> Fold 1 ... Fold 2 ... Fold 3 ... Fold 4 ... Fold 5 ... 
#> 
  |                                                                            
  |                                                                      |   0%

rex_test <- RexProcess(HdxData = DataFrame(BRD4_ibet),
                       params = rex_test,
                       range = 5:10,
                       thin = 1, whichChains = c(1,2))

rex_diff <- processDifferential(params = rex_test,
                                HdxData = DataFrame(BRD4_apo),
                                 whichChain = c(1))

gg1 <- plotVolcano(diff_params = rex_diff,
                   nrow = 5,
                   quantity = "TRE")
print(gg1)