DRomics: Dose Response for Omics

library(DRomics)
visualize <- FALSE # put to TRUE for a manual check of plots

if(visualize) 
{
  # (1) An example from data published by Larras et al. 2020
# in Journal of Hazardous Materials
# https://doi.org/10.1016/j.jhazmat.2020.122727

# a dataframe with metabolomic results (output $res of bmdcalc() or bmdboot() functions)
resfilename <- system.file("extdata", "triclosanSVmetabres.txt", package="DRomics")
res <- read.table(resfilename, header = TRUE, stringsAsFactors = TRUE)
str(res)

# a dataframe with annotation of each item identified in the previous file
# each item may have more than one annotation (-> more than one line)
annotfilename <- system.file("extdata", "triclosanSVmetabannot.txt", package="DRomics")
annot <- read.table(annotfilename, header = TRUE, stringsAsFactors = TRUE)
str(annot)

# Merging of both previous dataframes
# in order to obtain an extenderes dataframe
# bootstrap results and annotation
annotres <- merge(x = res, y = annot, by.x = "id", by.y = "metab.code")
head(annotres)

# Plots on the BMDxfold (with NA values)
sensitivityplot(annotres, BMDtype = "xfold",
                group = "path_class")

sensitivityplot(annotres, BMDtype = "xfold",
                group = "path_class", 
                BMDsummary = "median")

sensitivityplot(annotres, BMDtype = "xfold",
                group = "path_class", 
                BMDsummary = "median.and.IQR")

# after use of selectgroups
nrow(annotres)
annotres.s1 <- selectgroups(annotres, BMDtype = "xfold", 
                            group = "path_class", nitemsmin = 1)
nrow(annotres.s1)
sensitivityplot(annotres.s1, BMDtype = "xfold",
                group = "path_class")

# (2) 
# An example with two molecular levels
#
### Rename metabolomic results
metabextendedres <- annotres
str(metabextendedres)

# Import the dataframe with transcriptomic results 
contigresfilename <- system.file("extdata", "triclosanSVcontigres.txt", package = "DRomics")
contigres <- read.table(contigresfilename, header = TRUE, stringsAsFactors = TRUE)
str(contigres)

# Import the dataframe with functional annotation (or any other descriptor/category 
# you want to use, here KEGG pathway classes) 
contigannotfilename <- system.file("extdata", "triclosanSVcontigannot.txt", package = "DRomics")
contigannot <- read.table(contigannotfilename, header = TRUE, stringsAsFactors = TRUE)
str(contigannot)

# Merging of both previous dataframes   
contigextendedres <- merge(x = contigres, y = contigannot, by.x = "id", by.y = "contig")
# to see the structure of this dataframe
str(contigextendedres)

colnames(contigextendedres)
colnames(metabextendedres)

## sensitivityplot on BMDxfold on contigextendedres
sensitivityplot(contigextendedres, BMDtype = "xfold",
                group = "path_class")
nrow(contigextendedres)
contigextendedres.s1 <- selectgroups(contigextendedres,
                                     BMDtype = "xfold", 
                            group = "path_class", BMDmax = 2)
nrow(contigextendedres.s1)
sensitivityplot(contigextendedres.s1, BMDtype = "xfold",
                group = "path_class")

### Merge metabolomic and transcriptomic results
extendedres <- rbind(metabextendedres, contigextendedres)
extendedres$molecular.level <- factor(c(rep("metabolites", nrow(metabextendedres)),
                                        rep("contigs", nrow(contigextendedres))))
str(extendedres)

### Plot of 25th quantiles of BMD-zSD calculated by pathway
### and colored by molecular level
# optional inverse alphabetic ordering of groups for the plot
extendedres$path_class <- factor(extendedres$path_class, 
                                 levels = sort(levels(extendedres$path_class), 
                                               decreasing = TRUE))
sensitivityplot(extendedres, BMDtype = "zSD",
                group = "path_class", colorby = "molecular.level", 
                BMDsummary = "first.quartile")

### Plot of medians and IQRs of BMD-zSD 
sensitivityplot(extendedres, BMDtype = "zSD",
                group = "path_class", colorby = "molecular.level", 
                BMDsummary = "median.and.IQR")

### Plot of medians of BMD-zSD 
sensitivityplot(extendedres, BMDtype = "zSD",
                group = "path_class", colorby = "molecular.level", 
                BMDsummary = "median")

### Plot of first quartiles of BMD-xfold 
sensitivityplot(extendedres, BMDtype = "xfold",
                group = "path_class", colorby = "molecular.level", 
                BMDsummary = "first.quartile")

### Plot of medians of BMD-xfold 
sensitivityplot(extendedres, BMDtype = "xfold",
                group = "path_class", colorby = "molecular.level", 
                BMDsummary = "median")

### Plot of medians and IQRof BMD-xfold 
sensitivityplot(extendedres, BMDtype = "xfold",
                group = "path_class", colorby = "molecular.level", 
                BMDsummary = "median.and.IQR")

  
}