inst/doc/introduction.R

In tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse

## ---- 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 %>%
    tidy()

## -----------------------------------------------------------------------------
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(transcript) %>%
    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()