Sequencing depth per C1 chip

Setup

Total sequencing depth

Session information

Last updated: 2019-02-01

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✔ 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(12345)

The command set.seed(12345) 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.

✔ Repository version: 5b3779c

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:


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Untracked files:
    Untracked:  create-env.sh
    Untracked:  publish.bash
    Untracked:  snake.txt
    Untracked:  snakelog.out
    Untracked:  update-env.sh

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.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	5b3779c	John Blischak	2019-02-01	Update workflowr to 1.0.1 with wflow_update().
html	5b3779c	John Blischak	2019-02-01	Update workflowr to 1.0.1 with wflow_update().
html	da1fdf3	John Blischak	2018-02-06	Build site.
html	cf9e702	Joyce Hsiao	2017-12-13	Build site.
html	029305c	John Blischak	2017-12-04	Build site.
Rmd	6018090	pytung	2017-11-30	minor edits
html	6898149	John Blischak	2017-11-29	Build site.
Rmd	3d5d193	John Blischak	2017-11-29	Visualize sequencing depth per C1 chip.

Setup

library("dplyr")
library("DT")
library("ggplot2")
library("reshape2")
library("Biobase")
theme_set(cowplot::theme_cowplot())

fname <- Sys.glob("../data/eset/*.rds")
eset <- Reduce(combine, Map(readRDS, fname))
pData(eset)$experiment <- as.factor(pData(eset)$experiment)

Total sequencing depth

ggplot(pData(eset), aes(x = raw, color = experiment)) +
  geom_density() +
  labs(x = "Number of raw sequences per single cell", y = "Number of cells",
       title = "Distribution of total raw sequences per single cell") +
  scale_color_discrete(name = "C1 chip")

Expand here to see past versions of distribution-sequencing-depth-1.png:

Version	Author	Date
da1fdf3	John Blischak	2018-02-06
6898149	John Blischak	2017-11-29

Mapped reads per cell

ggplot(pData(eset), aes(x = experiment, y = mapped, color = experiment)) +
  geom_violin() + 
  geom_boxplot(alpha = .01, width = .2, position = position_dodge(width = .9)) +
  labs(x = "C1 chip", y = "Number of reads",
       title = "Number of mapped sequences per single cell") +
  theme(legend.title = element_blank(),
        axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))

Expand here to see past versions of mapped-1.png:

Version	Author	Date
da1fdf3	John Blischak	2018-02-06
029305c	John Blischak	2017-12-04

Sum of sequences across the 96 single cells per C1 chip.

total_per_experiment <- pData(eset) %>%
  group_by(experiment) %>%
  summarize(raw = sum(raw) / 10^6,
            mapped = sum(mapped) / 10^6,
            molecules = sum(molecules) / 10^6)
datatable(total_per_experiment,
          options = list(pageLength = nrow(total_per_experiment)),
          colnames = c("C1 chip", "Number of raw sequences",
                       "Number of mapped",
                       "Number of molecules"))

Show entries

Search:

	C1 chip	Number of raw sequences	Number of mapped	Number of molecules
1	20170905	380.687736	177.84221	10.036337
2	20170906	362.73125	163.976187	10.877239
3	20170907	371.427564	155.019309	9.593111
4	20170908	412.542083	154.324245	12.324649
5	20170910	436.002711	167.100997	12.568274
6	20170912	414.087135	176.894625	12.285908
7	20170913	409.345623	145.720572	9.416785
8	20170914	387.607724	160.274388	11.743803
9	20170915	394.864013	142.408214	11.926311
10	20170916	396.638177	128.065458	11.656424
11	20170917	365.420416	161.328501	9.872018
12	20170919	385.569765	152.399081	11.313303
13	20170920	384.111251	162.471812	10.755671
14	20170921	410.999651	175.334635	13.492618
15	20170922	403.666478	136.584871	10.561215
16	20170924	371.133791	178.332344	12.572015

Showing 1 to 16 of 16 entries

Previous1Next

ggplot(melt(total_per_experiment, id.vars = "experiment",
            variable.name = "type", value.name = "count"),
       aes(x = experiment, y = count, color = type)) +
  geom_point() +
  labs(title = "Sequencing depth per C1 chip",
       x = "C1 chip", y = "Number of sequences") +
  theme(legend.title = element_blank(),
        axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1))

Expand here to see past versions of unnamed-chunk-1-1.png:

Version	Author	Date
da1fdf3	John Blischak	2018-02-06
029305c	John Blischak	2017-12-04
6898149	John Blischak	2017-11-29

Session information

sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS: /project2/gilad/jdblischak/miniconda3/envs/fucci-seq/lib/R/lib/libRblas.so
LAPACK: /project2/gilad/jdblischak/miniconda3/envs/fucci-seq/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] bindrcpp_0.2        Biobase_2.38.0      BiocGenerics_0.24.0
[4] reshape2_1.4.2      ggplot2_2.2.1       DT_0.2             
[7] dplyr_0.7.4        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13      compiler_3.4.1    git2r_0.19.0     
 [4] plyr_1.8.4        workflowr_1.0.1   bindr_0.1        
 [7] R.methodsS3_1.7.1 R.utils_2.5.0     tools_3.4.1      
[10] digest_0.6.12     jsonlite_1.4      evaluate_0.10.1  
[13] tibble_1.3.3      gtable_0.2.0      pkgconfig_2.0.1  
[16] rlang_0.1.2       yaml_2.1.14       stringr_1.2.0    
[19] knitr_1.16        htmlwidgets_0.9   cowplot_0.9.1    
[22] rprojroot_1.2     grid_3.4.1        glue_1.1.1       
[25] R6_2.2.0          rmarkdown_1.8     magrittr_1.5     
[28] whisker_0.3-2     backports_1.0.5   scales_0.5.0     
[31] htmltools_0.3.6   assertthat_0.1    colorspace_1.3-2 
[34] labeling_0.3      stringi_1.1.2     lazyeval_0.2.0   
[37] munsell_0.4.3     R.oo_1.21.0

This reproducible R Markdown analysis was created with workflowr 1.0.1

Sequencing depth per C1 chip

John Blischak

2017-11-28

Setup

Total sequencing depth

Session information