## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----options, results='hide', message=FALSE, eval=TRUE, echo=FALSE--------- library(Xeva) ## ----get_lib, results='hide', message=FALSE, eval=FALSE-------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Xeva", version = "3.8") ## ----githubInst, results='hide', message=FALSE, eval=FALSE----------------- # #install devtools if required # install.packages("devtools") # # #install Xeva as: # devtools::install_github("bhklab/Xeva") ## ----l, results='hide', message=FALSE, eval=TRUE--------------------------- library(Xeva) ## ----biobase, results='hide', message=FALSE, eval=TRUE, echo=FALSE--------- suppressMessages(library(Biobase)) ## ----l2-------------------------------------------------------------------- data(brca) print(brca) ## ----l3-------------------------------------------------------------------- brca.mod <- modelInfo(brca) dim(brca.mod) brca.mod[1:4, ] ## ----expre----------------------------------------------------------------- model.data <- getExperiment(brca, model.id = "X.1004.BG98") head(model.data) ## ----batch1---------------------------------------------------------------- batch.name <- batchInfo(brca) batch.name[1:4] ## ----batch2---------------------------------------------------------------- batchInfo(brca, batch = "X-1004.binimetinib") ## ----plot1, fig.cap="Tumor growth curves for a batch of control and treated PDXs", out.width='4in', fig.wide=TRUE---- plotPDX(brca, batch = "X-4567.BKM120") ## ----pdxplot2, fig.cap="Tumor growth curves for a batch of control and treated PDXs. Here, the volume is normalized and plots are truncated at 40 days", out.width='4in', fig.wide=TRUE---- plotPDX(brca, batch = "X-4567.BKM120", vol.normal = TRUE, control.col = "#a6611a", treatment.col = "#018571", major.line.size = 1, max.time = 40) ## ----pdxplot3, fig.cap="Tumor growth curves for a batch of control and treated PDXs generated using patient ID and drug name", out.width='4in', fig.wide=TRUE---- plotPDX(brca, patient.id="X-3078", drug="paclitaxel",control.name = "untreated") ## ----repplot1, fig.cap="Tumor growth curves for a batch of control and treated PDXs with replicates", out.width='4in', fig.wide=TRUE---- data("repdx") plotPDX(repdx, vol.normal = TRUE, batch = "P1") ## ----repplot2, fig.cap="Errorbar visualization for tumor growth curves of a PDX batch", out.width='4in', fig.wide=TRUE---- plotPDX(repdx, batch = "P3", SE.plot = "errorbar") ## ----repplot3, fig.cap="Ribbon visualization for tumor growth curves of a PDX batch", out.width='4in', fig.wide=TRUE---- plotPDX(repdx, batch = "P4", vol.normal = TRUE, SE.plot = "ribbon") ## ----l4-------------------------------------------------------------------- brca.mr <- summarizeResponse(brca, response.measure = "mRECIST") brca.mr[1:5, 1:4] ## ----mR_BRCA, fig.cap="mRECIST plot for PDXE breast cancer data", fig.width=14.1, fig.height=7.8, fig.wide=TRUE---- plotmRECIST(brca.mr, control.name="untreated", row_fontsize=13, col_fontsize=12) ## ----waterFall1, fig.cap="Waterfall plot for binimetinib drug response in PDXs", fig.width=14.1, fig.height=7.8, fig.wide=TRUE---- waterfall(brca, drug="binimetinib", res.measure="best.average.response") ## ----waterFall2, fig.cap="Waterfall plot for BYL719 drug response in PDXs", fig.width=14.1, fig.height=7.8, fig.wide=TRUE---- mut <- summarizeMolecularProfiles(brca,drug = "BYL719", mDataType="mutation") model.type <- Biobase::exprs(mut)["CDK13", ] model.type[grepl("Mut", model.type)] <- "mutation" model.type[model.type!="mutation"] <- "wild type" model.color <- list("mutation"="#b2182b", "wild type"="#878787") waterfall(brca, drug="BYL719", res.measure="best.average.response", model.id=names(model.type), model.type= model.type, type.color = model.color) ## ----response1------------------------------------------------------------- data("repdx") response(repdx, batch="P1", res.measure="angle") ## ----response2------------------------------------------------------------- data("repdx") response(repdx, batch="P1", res.measure="lmm") ## ----biomarker1------------------------------------------------------------ data(brca) drugSensitivitySig(object=brca, drug="tamoxifen", mDataType="RNASeq", features=c(1,2,3,4,5), sensitivity.measure="slope", fit="lm") ## ----biomarker2------------------------------------------------------------ data(brca) drugSensitivitySig(object=brca, drug="tamoxifen", mDataType="RNASeq", features=c(1,2,3,4,5), sensitivity.measure="best.average.response", fit = "lm") ## ----biomarker3, warning=FALSE--------------------------------------------- data(brca) drugSensitivitySig(object=brca, drug="tamoxifen", mDataType="RNASeq", features=c(1,2,3,4,5), sensitivity.measure="best.average.response", fit="pearson") ## ----x1-------------------------------------------------------------------- model=read.csv(system.file("extdata", "model.csv", package = "Xeva")) head(model) ## ----x2-------------------------------------------------------------------- drug=read.csv(system.file("extdata", "drug.csv", package = "Xeva")) head(drug) ## ----x3-------------------------------------------------------------------- experiment=read.csv(system.file("extdata","experiments.csv",package="Xeva")) head(experiment) ## ----x4-------------------------------------------------------------------- expDesign=readRDS(system.file("extdata","batch_list.rds",package="Xeva")) expDesign[[1]] ## ----x5-------------------------------------------------------------------- RNASeq=readRDS(system.file("extdata", "rnaseq.rds", package = "Xeva")) print(RNASeq) ## ----x6-------------------------------------------------------------------- modToBiobaseMap=read.csv(system.file("extdata","modelToExpressionMap.csv", package = "Xeva")) head(modToBiobaseMap) ## ----createXevaSet--------------------------------------------------------- xeva.set=createXevaSet(name="example xevaSet", model=model, drug=drug, experiment=experiment, expDesign=expDesign, molecularProfiles=list(RNASeq = RNASeq), modToBiobaseMap = modToBiobaseMap) print(xeva.set) ## ----sess------------------------------------------------------------------ sessionInfo()