Read to molecule conversion

Last updated: 2020-01-23

Checks: 7 0

Knit directory: peco-paper/

This reproducible R Markdown analysis was created with workflowr (version 1.6.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20190814)

The command set.seed(20190814) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: fdc569c

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/npreg_trendfilter_quantile.Rmd
    Untracked:  code/fig2_rev.R
    Untracked:  data/fit.quant.rds
    Untracked:  data/log2cpm.quant.rds

Unstaged changes:
    Modified:   analysis/access_data.Rmd
    Modified:   analysis/index.Rmd
    Modified:   code/fig2.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	fdc569c	jhsiao999	2020-01-23	move reads-v-molecules.Rmd and change eset to sce

Setup

library("cowplot")
library("dplyr")
library("DT")
library("ggplot2")
library("reshape2")
library("SingleCellExperiment")
theme_set(theme_cowplot())

sce_raw = readRDS("data/sce-raw.rds")
anno = data.frame(colData(sce_raw))
anno$experiment = factor(anno$experiment)

Reads versus molecules

conv_hs_c1 <- ggplot(anno, aes(x = reads_hs, y = mol_hs,
                                     color = experiment)) +
  geom_point(alpha = 1/2) +
  labs(x = "Total read count",
       y = "Total molecule count",
       title = "Endogenous genes by C1 chip") +
  theme(legend.position = "none")

conv_hs_ind <- ggplot(anno, aes(x = reads_hs, y = mol_hs,
                                      color = chip_id)) +
  geom_point(alpha = 1/2) +
  scale_color_brewer(palette = "Dark2") +
  labs(x = "Total read count",
       y = "Total molecule count",
       title = "Endogenous genes by individual") +
  theme(legend.position = "none")

conv_ercc_c1 <- ggplot(anno, aes(x = reads_ercc, y = mol_ercc,
                                        color = experiment)) +
  geom_point(alpha = 1/2) +
  labs(x = "Total read count",
       y = "Total molecule count",
       title = "ERCC genes by C1 chip") +
  theme(legend.position = "none")

conv_ercc_ind <- ggplot(anno, aes(x = reads_ercc, y = mol_ercc,
                                         color = chip_id)) +
  geom_point(alpha = 1/2) +
  scale_color_brewer(palette = "Dark2") +
  labs(x = "Total read count",
       y = "Total molecule count",
       title = "ERCC genes by individual") +
  theme(legend.position = "none")

plot_grid(conv_hs_c1, conv_hs_ind, conv_ercc_c1, conv_ercc_ind,
        labels = letters[1:4])