## ----style, echo=FALSE, results="asis", message=FALSE----------------------
knitr::opts_chunk$set(tidy = FALSE,
                      warning = FALSE,
                      message = FALSE)

## ----install, eval=FALSE, warning=FALSE------------------------------------
#  if (!require("BiocManager")) {
#      install.packages("BiocManager")
#  }
#  BiocManager::install("RNASeqRData")

## ----fig.width=10,  echo=FALSE---------------------------------------------
library(png)
library(grid)
img <- readPNG("figure/whole_file_structure.png")
grid.raster(img, just = "center")

## ----fig.width=10, echo=FALSE----------------------------------------------
img <- readPNG("figure/input_files_structure.png")
grid.raster(img, just = "center")

## ---- warning=FALSE--------------------------------------------------------
library(RNASeqR)
library(RNASeqRData)

## --------------------------------------------------------------------------
input_files.path <- system.file("extdata/", package = "RNASeqRData")
rnaseq_result.path <- tempdir(check = TRUE)
list.files(input_files.path, recursive = TRUE)

## ---- warning=FALSE--------------------------------------------------------
exp <- RNASeqRParam(path.prefix = rnaseq_result.path, 
                    input.path.prefix = input_files.path, 
                    genome.name = "Saccharomyces_cerevisiae_XV_Ensembl", 
                    sample.pattern = "SRR[0-9]*_XV",
                    independent.variable = "state", 
                    case.group = "60mins_ID20_amphotericin_B", 
                    control.group = "60mins_ID20_control")

## ---- warning=FALSE--------------------------------------------------------
show(exp)

## ---- eval=FALSE-----------------------------------------------------------
#  RNASeqEnvironmentSet_CMD(exp)

## ---- warning=FALSE--------------------------------------------------------
RNASeqEnvironmentSet(exp)

## ----fig.width=20, echo=FALSE----------------------------------------------
img <- readPNG("figure/fastqReport.png")
grid.raster(img, just = "center")

## ---- eval=FALSE-----------------------------------------------------------
#  RNASeqQualityAssessment_CMD(exp)

## ---- warning=FALSE--------------------------------------------------------
RNASeqQualityAssessment(exp)

## ----fig.width=6,fig.height=6, echo=FALSE----------------------------------
img <- readPNG("figure/Alignment_Report/Alignment_Result_ggplot2.png")
grid.raster(img, just = "center")

## ----fig.width=6,fig.height=6, echo=FALSE----------------------------------
img <- readPNG("figure/Alignment_Report/Overall_Mapping_rate_ggplot2.png")
grid.raster(img, just = "center")

## ---- eval=FALSE-----------------------------------------------------------
#  RNASeqReadProcess_CMD(exp)

## ---- warning=FALSE--------------------------------------------------------
RNASeqReadProcess(exp)

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Frequency/Frequency_Plot_normalized_count_ggplot2.png")
 grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Frequency/Frequency_Plot_log_normalized_count_ggplot2.png")
 grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Distribution/Box_Plot_ggplot2.png")
 grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Distribution/Violin_Plot_ggplot2.png")
 grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/PCA/Dimension_PCA_Plot_factoextra.png")
 grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/PCA/PCA_Plot_factoextra.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/PCA/PCA_Plot_ggplot2.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Correlation/Correlation_Heat_Plot_ggplot2.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Correlation/Correlation_Dot_Plot_corrplot.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Correlation/Correlation_Bar_Plot_PerformanceAnalytics.png")
grid.raster(img, just = "center")

## ----fig.width=8, fig.height=8, echo=FALSE---------------------------------
img <- readPNG("figure/DE/Volcano_Plot_graphics.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/DE/PCA/Dimension_PCA_Plot_factoextra.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/DE/PCA/PCA_Plot_factoextra.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/DE/PCA/PCA_Plot_ggplot2.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/DE/Heatmap_Plot_pheatmap.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/transcript_related/Distribution_Transcript_Count_per_Gene_Plot.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/transcript_related/Distribution_Transcript_Length_Plot.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/ballgown_MA_Plot_ggplot2.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/preDE/Dispersion_Plot_DESeq2.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/DE/MA_Plot_DESeq2.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/edgeR_MeanVar_Plot_edgeR.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/edgeR_BCV_Plot_edgeR.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/edgeR_MDS_Plot_edgeR.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/edgeR_Smear_Plot_edgeR.png")
grid.raster(img, just = "center")

## ---- eval=FALSE-----------------------------------------------------------
#  RNASeqDifferentialAnalysis_CMD(exp)

## ---- warning=FALSE--------------------------------------------------------
RNASeqDifferentialAnalysis(exp)

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/GO_analysis/GO_CC_Classification_Bar_Plot_clusterProfiler.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/GO_analysis/GO_MF_Overrepresentation_Bar_Plot_clusterProfiler.png")
grid.raster(img, just = "center")

## ----fig.width=6, height=6, echo=FALSE-------------------------------------
img <- readPNG("figure/GO_analysis/GO_MF_Overrepresentation_Dot_Plot_clusterProfiler.png")
grid.raster(img, just = "center")

## ---- eval = FALSE---------------------------------------------------------
#  RNASeqGoKegg_CMD(exp,
#                   OrgDb.species = "org.Sc.sgd.db",
#                   go.level = 3,
#                   input.TYPE.ID = "GENENAME",
#                   KEGG.organism = "sce")

## ---- warning=FALSE--------------------------------------------------------
RNASeqGoKegg(exp, 
             OrgDb.species = "org.Sc.sgd.db", 
             go.level = 3, 
             input.TYPE.ID = "GENENAME",
             KEGG.organism = "sce")

## --------------------------------------------------------------------------
sessionInfo()