## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo=TRUE) ## ---- eval=TRUE, echo = FALSE, include=TRUE, message=FALSE, warning=FALSE----- library(bigPint) data("soybean_cn_sub") ret <- plotSM(data=soybean_cn_sub, saveFile = FALSE) ret[["S1_S2"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, message=FALSE, warning=FALSE----- data("soybean_cn_sub_metrics") ret <- plotSM(data=soybean_cn_sub, dataMetrics = soybean_cn_sub_metrics, pointColor = "magenta", saveFile = FALSE) ret[["S1_S2"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, message=FALSE, warning=FALSE----- soybean_cn_sub_st <- as.data.frame(t(apply(as.matrix(soybean_cn_sub[,-1]), 1, scale))) soybean_cn_sub_st$ID <- as.character(soybean_cn_sub$ID) soybean_cn_sub_st <- soybean_cn_sub_st[,c(length(soybean_cn_sub_st), 1:length(soybean_cn_sub_st)-1)] colnames(soybean_cn_sub_st) <- colnames(soybean_cn_sub) nID <- which(is.nan(soybean_cn_sub_st[,2])) soybean_cn_sub_st[nID,2:length(soybean_cn_sub_st)] <- 0 ret <- plotSM(data=soybean_cn_sub_st, dataMetrics = soybean_cn_sub_metrics, pointColor = "magenta", saveFile = FALSE) ret[["S1_S2"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, warning=FALSE, fig.width = 7.2916667, fig.asp= 1/1.618---- geneList = soybean_cn_sub_metrics[["S1_S2"]][1:5,]$ID ret <- plotLitre(data = soybean_cn_sub[,c(1:7)], geneList = geneList, pointColor = "gold", saveFile = FALSE, pointSize = 2) ret[["S1_S2_Glyma18g00690.1"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, warning=FALSE, fig.width = 7.2916667, fig.asp= 1/1.618---- geneList = soybean_cn_sub_metrics[["S1_S2"]][7327:7332,]$ID ret <- plotLitre(data = soybean_cn_sub[,c(1:7)], geneList = geneList, pointColor = "gold", saveFile = FALSE, pointSize = 2) ret[["S1_S2_Glyma05g34410.3"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, warning=FALSE, fig.width = 7.2916667, fig.asp= 1/1.618---- geneList = soybean_cn_sub_metrics[["S1_S2"]][1:5,]$ID ret <- plotLitre(data = soybean_cn_sub_st[,c(1:7)], geneList = geneList, pointColor = "gold", saveFile = FALSE, pointSize = 3) ret[["S1_S2_Glyma18g00690.1"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, warning=FALSE, fig.width = 7.2916667, fig.asp= 1/1.618---- geneList = soybean_cn_sub_metrics[["S1_S2"]][7327:7332,]$ID ret <- plotLitre(data = soybean_cn_sub_st[,c(1:7)], geneList = geneList, pointColor = "gold", saveFile = FALSE, pointSize = 3) ret[["S1_S2_Glyma05g34410.3"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, warning=FALSE, fig.width = 7.2916667, fig.asp= 1/1.618---- ret <- plotPCP(data = soybean_cn_sub_st, dataMetrics = soybean_cn_sub_metrics, saveFile = FALSE, lineSize = 0.5) ret[["S1_S2"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, warning=FALSE, fig.width = 7.2916667, fig.asp= 1/1.618---- geneList <- tail(soybean_cn_sub_metrics[["S1_S2"]], 16)$ID ret <- plotPCP(data = soybean_cn_sub_st, geneList = geneList, saveFile = FALSE, lineSize = 0.5) ret[["S1_S2"]] ## ---- eval=TRUE, echo = FALSE, include=TRUE, message=FALSE, warning=FALSE, fig.width = 7.2916667, fig.asp= 1/1.618---- ret <- plotVolcano(data = soybean_cn_sub, dataMetrics = soybean_cn_sub_metrics, saveFile = FALSE, pointSize = 3, pointColor = "red") ret[["S1_S2"]]