## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo=TRUE)

## ---- eval=TRUE, include=TRUE, message=FALSE----------------------------------
library(bigPint)
data("soybean_ir_sub")
data("soybean_ir_sub_metrics")
soybean_ir_sub[,-1] <- log(soybean_ir_sub[,-1] + 1)
ret <- plotSM(data=soybean_ir_sub, dataMetrics=soybean_ir_sub_metrics,
  threshVar = "FDR", threshVal = 1e-10, pointSize = 0.1, saveFile = FALSE)
ret[["N_P"]]

## ---- eval=TRUE, include=TRUE, message=FALSE, warning=FALSE-------------------
library(dplyr)
sigGenes = soybean_ir_sub_metrics[["N_P"]] %>% filter(FDR < 1e-10) %>% select(ID)
sigGenes = sigGenes[,1]
ret <- plotSM(data=soybean_ir_sub, geneList = sigGenes, pointSize = 0.1,
  saveFile = FALSE)
ret[["N_P"]]

## ---- eval=TRUE, include=TRUE-------------------------------------------------
library(dplyr)
sigGenes = soybean_ir_sub_metrics[["N_P"]] %>% filter(FDR < 1e-10) %>%   
  filter(abs(logFC) > 6) %>% select(ID)
sigGenes = sigGenes[,1]
ret <- plotSM(data=soybean_ir_sub, geneList = sigGenes, pointSize = 0.5,
  pointColor = "magenta", saveFile = FALSE)
ret[["N_P"]]

## ---- eval=TRUE, include=TRUE-------------------------------------------------
ret <- plotSM(data=soybean_ir_sub, saveFile = FALSE)
ret[["N_P"]]