## ---- echo=FALSE, include=FALSE----------------------------------------------- library(knitr) knitr::opts_chunk$set(warning=FALSE, message=FALSE) ## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("tidySummarizedExperiment") ## ---- eval=FALSE-------------------------------------------------------------- # devtools::install_github("stemangiola/tidySummarizedExperiment") ## ----------------------------------------------------------------------------- library(ggplot2) library(tidySummarizedExperiment) ## ----------------------------------------------------------------------------- pasilla_tidy <- tidySummarizedExperiment::pasilla ## ----------------------------------------------------------------------------- pasilla_tidy ## ----------------------------------------------------------------------------- Assays(pasilla_tidy) ## ----------------------------------------------------------------------------- pasilla_tidy %>% slice(1) ## ----------------------------------------------------------------------------- pasilla_tidy %>% filter(condition == "untreated") ## ----------------------------------------------------------------------------- pasilla_tidy %>% select(sample) ## ----------------------------------------------------------------------------- pasilla_tidy %>% count(sample) ## ----------------------------------------------------------------------------- pasilla_tidy %>% distinct(sample, condition, type) ## ----------------------------------------------------------------------------- pasilla_tidy %>% rename(sequencing=type) ## ----------------------------------------------------------------------------- pasilla_tidy %>% mutate(type=gsub("_end", "", type)) ## ----------------------------------------------------------------------------- pasilla_tidy %>% unite("group", c(condition, type)) ## ----------------------------------------------------------------------------- pasilla_tidy %>% group_by(sample) %>% summarise(total_counts=sum(counts)) ## ----------------------------------------------------------------------------- pasilla_tidy %>% group_by(feature) %>% mutate(mean_count=mean(counts)) %>% filter(mean_count > 0) ## ----------------------------------------------------------------------------- my_theme <- list( scale_fill_brewer(palette="Set1"), scale_color_brewer(palette="Set1"), theme_bw() + theme( panel.border=element_blank(), axis.line=element_line(), panel.grid.major=element_line(size=0.2), panel.grid.minor=element_line(size=0.1), text=element_text(size=12), legend.position="bottom", aspect.ratio=1, strip.background=element_blank(), axis.title.x=element_text(margin=margin(t=10, r=10, b=10, l=10)), axis.title.y=element_text(margin=margin(t=10, r=10, b=10, l=10)) ) ) ## ----plot1-------------------------------------------------------------------- pasilla_tidy %>% tidySummarizedExperiment::ggplot(aes(counts + 1, group=sample, color=`type`)) + geom_density() + scale_x_log10() + my_theme ## ----------------------------------------------------------------------------- sessionInfo()