test/test_obsPlot.R

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

# Test tidyContrasts, logRatioPlot, tidyIntensity and obsPlot2

library(DGEobj)
library(DGE.Tools2)
library(tidyverse)
library(magrittr)
library(JRTutil)

stashRoot <- getStashPath()
stashPath <- file.path(stashRoot, "data/nonclin/DGEobj_library")
dgeObj <- readRDS(file.path(stashPath, "BDL_Rat_LiverSlice_P-20170808-0001_03Dec2017.RDS"))

# saveRDS (dgeObj, "../BDL_Rat_LiverSlice_P-20170808-0001_03Dec2017.RDS")
# dgeObj <- readRDS("../BDL_Rat_LiverSlice_P-20170808-0001_03Dec2017.RDS")

#filter DGEobj for Lpar* gene family
idx <- str_detect(dgeObj$geneData$GeneName, "^Lpar")
dgeObj_filt <- dgeObj[idx,]

#get EnsgID to GeneSymbol map
ga <- dgeObj_filt$geneData %>%
  rownames_to_column(var="EnsgID") %>%
  select(EnsgID, GeneSymbol=GeneName)

tcDat <-tidyContrasts(dgeObj_filt, rownameColumn="EnsgID", includeColumns = c("logFC", "CI.R", "CI.L"))
#add gene symbols to tcDat
tcDat %<>% left_join(ga)

# #prep data for nondescript example
# #rename the contrasts
# tcDat$Contrast <- str_c("Contrast", sort(rep(1:4,4)))
# #replace the geneIDs
# tcDat$EnsgID <- str_c("Gene", rep(1:4,4))
# #round the numbers
# tcDat[,2:4] <- round(tcDat[,2:4], 3)
# #drop GeneSymbol
# tcDat$GeneSymbol <- NULL
# dput(tcDat)

##let's plot lpar gene family
# idx <- str_detect(ga$GeneSymbol, "^Lpar")
# GOI <- ga$GeneSymbol[idx]
# tcDat %<>% filter(GeneSymbol %in% GOI)
# unique(tcDat$Contrast)


#now plot logratio +/- CI
MyPlot <- logRatioPlot(tcDat, plotType="point",
                       facetColname = "GeneSymbol",
                       xColname = "Contrast",
                       facetCol=4,
                       scales="fixed",
                       facet=TRUE,
                       title = "Test",
                       pointSize=4,
                       lineLayer=TRUE,
                       lineSize=0.1,
                       xAngle=60,
                       ylab = "Log2Ratio")

#now plot logratio +/- CI
MyPlot <- logRatioPlot(tcDat,
                       facetColname = "GeneSymbol",
                       xColname = "Contrast",
                       facetCol = 4,
                       scales = "fixed",
                       barWidth = 0.7)

####################################################
#####  Intensity Plots
log2cpm <- convertCounts(dgeObj$counts, unit="cpm", log=TRUE, normalize="tmm")


#filter for genes of interest
##let's plot lpar gene family
idx <- rownames(log2cpm) %in% ga$EnsgID
log2cpm <- log2cpm[idx,]

tiDat <- tidyIntensity(log2cpm,
                       rowidColname ="EnsgID",
                       keyColname="Contrast",
                       valueColname = "Log2CPM",
                       group=dgeObj$design$ReplicateGroup)
#add gene symbols
tiDat %<>% left_join(ga)

#facetted plot
myplot <- obsPlot2(tiDat, plotByCol="GeneSymbol",
                   groupCol="group",
                   valueCol="Log2CPM",
                   scale="fixed",
                   facetRow=2,
                   meanSize=2)
myplot

#Individual Plots
myplot <- obsPlot2(tiDat, plotByCol="GeneSymbol",
                   groupCol="group",
                   valueCol="Log2CPM",
                   scale="fixed",
                   facet = FALSE,
                   meanSize=2)
myplot[[1]]