Rex butterfly plots for differential analysis

Rex butterfly plots for differential analysis

plotButterfly(diff_params, nrow = 5, quantity = "TRE", interval = NULL)

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 "signedARE"

interval

The interval to plot (Residues)

Value

Returns a ggplot object

Examples

require(RexMS)
require(dplyr)
require(ggplot2)
#> Loading required package: 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 <- plotButterfly(diff_params = rex_diff,
                   nrow = 5,
                   quantity = "TRE")
print(gg1)