## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("ERSSA") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/GTEx/ERSSA_plot_1_NumOfDEGenes_N10_title.png") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/GTEx/ERSSA_plot_1_NumOfDEGenes_N25_title.png") ## ----------------------------------------------------------------------------- library(ERSSA) # GTEx dataset with 10 heart and 10 muscle samples # "full"" dataset contains all ensembl genes data(condition_table.full) data(count_table.full) # For test purposes and faster run time, we will use a smaller "partial" dataset # 4 heart and 4 muscle samples # partial dataset contains 1000 genes data(condition_table.partial) data(count_table.partial) # NOTE: the figures are generated from the "full" dataset ## ----------------------------------------------------------------------------- head(count_table.full[,1:2]) ## ----------------------------------------------------------------------------- condition_table.full ## ----message=FALSE, warning=FALSE--------------------------------------------- set.seed(1) # for reproducible subsample generation ssa = erssa(count_table.partial, condition_table.partial, DE_ctrl_cond='heart') # Running full dataset is skipped in the interest of run time # ssa = erssa(count_table.full, condition_table.full, DE_ctrl_cond='heart') ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/GTEx/ERSSA_plot_1_NumOfDEGenes.png") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/GTEx/ERSSA_plot_2_MarginalNumOfDEGenes.png") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/GTEx/ERSSA_plot_3_IntersectDEGenes.png") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/GTEx/ERSSA_plot_4_FPRvTPRPlot.png") ## ----message=FALSE, warning=FALSE--------------------------------------------- library(ggplot2) # Parse out plot 1 de_plot = ssa$gg.dotPlot.obj$gg_object # Change y-axis label to be more descriptive de_plot = de_plot + ylab('Number of differentially expressed genes') # Save the plot in the current working directory with new dimensions and a # lower resolution. ggsave(filename='ERSSA_plot_1_NumOfDEGenes.png', plot=de_plot, dpi=100, width = 15, height = 10, units = "cm") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/GTEx/ERSSA_plot_1_NumOfDEGenes_lowRes.png") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/MP/ERSSA_plot_1_NumOfDEGenes.png") knitr::include_graphics("Figures/MP/ERSSA_plot_2_MarginalNumOfDEGenes.png") knitr::include_graphics("Figures/MP/ERSSA_plot_3_IntersectDEGenes.png") knitr::include_graphics("Figures/MP/ERSSA_plot_4_FPRvTPRPlot.png") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/Fossum/ERSSA_plot_1_NumOfDEGenes_AbslogFC1_title.png") ## ----out.width = "500px", echo=FALSE, fig.align = "center"-------------------- knitr::include_graphics("Figures/Fossum/ERSSA_plot_1_NumOfDEGenes_AbslogFC0.5_title.png") knitr::include_graphics("Figures/Fossum/ERSSA_plot_2_MarginalNumOfDEGenes.png") knitr::include_graphics("Figures/Fossum/ERSSA_plot_3_IntersectDEGenes.png") knitr::include_graphics("Figures/Fossum/ERSSA_plot_4_FPRvTPRPlot.png") ## ----------------------------------------------------------------------------- sessionInfo()