## ----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") ## ----fig.width=10, echo=FALSE---------------------------------------------- img <- readPNG("figure/phenodata_csv.png") grid.raster(img, just = "center") ## ---- warning=FALSE-------------------------------------------------------- library(RNASeqR) library(RNASeqRData) ## -------------------------------------------------------------------------- input_files.path <- system.file("extdata/", package = "RNASeqRData") #rnaseq_result.path <- "/Users/chaokuan-hao/Documents/ANU_2019_Semester_2/Lanfear_Lab/HI" rnaseq_result.path <- "/tmp/RNASeqR/" dir.create(rnaseq_result.path, recursive = 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", fastq.gz.type = "PE") ## ---- warning=FALSE, eval=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", # fastq.gz.type = "SE") ## ---- 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) ## ---- warning=FALSE, eval=FALSE-------------------------------------------- # Update_Fastq_gz (RNASeqRParam = exp, # prepared_fastq_gz = paste0(input_files.path, # "/input_files/raw_fastq.gz/"), # target_samples = "ALL") ## ----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) ## ---- eval=FALSE----------------------------------------------------------- # RNASeqReadProcess_CMD(exp, STAR.Alignment.run=TRUE, # Hisat2.Index.run=FALSE, # Hisat2.Alignment.run = FALSE) ## ---- warning=FALSE-------------------------------------------------------- RNASeqReadProcess(exp) ## ---- eval=FALSE----------------------------------------------------------- # RNASeqReadProcess(exp, STAR.Alignment.run=TRUE, # Hisat2.Index.run=FALSE, # Hisat2.Alignment.run = FALSE) ## ----fig.width=6, height=6, echo=FALSE------------------------------------- img <- readPNG("figure/DE/Statistical_Results.png") grid.raster(img, just = "center") ## ----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") ## ---- warning=FALSE, eval=FALSE-------------------------------------------- # exp_Sam <- RNASeqRParam_Sam(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, eval=FALSE-------------------------------------------- # exp_Bam <- RNASeqRParam_Bam(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, eval=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", # fastq.gz.type = "PE") ## ---- warning=FALSE, eval=FALSE-------------------------------------------- # RNASeqEnvironmentSet(exp) ## ---- warning=FALSE, eval=FALSE-------------------------------------------- # All_Steps_Interface_CMD(exp, # OrgDb.species = "org.Sc.sgd.db", # go.level = 3, # input.TYPE.ID = "GENENAME", # KEGG.organism = "sce") ## ---- warning=FALSE, eval=FALSE-------------------------------------------- # All_Steps_Interface(exp, # OrgDb.species = "org.Sc.sgd.db", # go.level = 3, # input.TYPE.ID = "GENENAME", # KEGG.organism = "sce") ## -------------------------------------------------------------------------- sessionInfo()