Last updated: 2019-02-01

workflowr checks: (Click a bullet for more information)
  • R Markdown file: uncommitted changes The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

  • 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: b467002

    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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        Ignored:    slurm-50625533.out
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        Ignored:    slurm-50625801.out
        Ignored:    slurm-50625803.out
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        Ignored:    slurm-50625928.out
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        Ignored:    slurm-50625939.out
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        Ignored:    slurm-50626614.out
        Ignored:    slurm-50626616.out
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        Ignored:    slurm-50627750.out
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        Ignored:    slurm-50627773.out
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        Ignored:    slurm-50627790.out
        Ignored:    slurm-50627798.out
        Ignored:    slurm-50627807.out
        Ignored:    slurm-50627815.out
        Ignored:    slurm-50627824.out
        Ignored:    slurm-50627833.out
        Ignored:    slurm-50627843.out
        Ignored:    slurm-50627851.out
        Ignored:    slurm-50627858.out
        Ignored:    slurm-50627867.out
        Ignored:    slurm-50627873.out
        Ignored:    slurm-50627881.out
        Ignored:    slurm-50627886.out
        Ignored:    slurm-50627889.out
        Ignored:    slurm-50627895.out
        Ignored:    slurm-50627904.out
        Ignored:    slurm-50627907.out
        Ignored:    slurm-50627909.out
        Ignored:    slurm-50627911.out
        Ignored:    slurm-50627915.out
        Ignored:    slurm-50627916.out
        Ignored:    slurm-50627918.out
        Ignored:    slurm-50627922.out
        Ignored:    slurm-50627928.out
        Ignored:    slurm-50627951.out
        Ignored:    slurm-50627976.out
        Ignored:    slurm-50627995.out
        Ignored:    slurm-50628022.out
        Ignored:    slurm-50628045.out
        Ignored:    slurm-50628067.out
        Ignored:    slurm-50628081.out
        Ignored:    slurm-50628089.out
        Ignored:    slurm-50628099.out
        Ignored:    slurm-50628106.out
        Ignored:    slurm-50628112.out
        Ignored:    slurm-50628121.out
        Ignored:    slurm-50628129.out
        Ignored:    slurm-50628135.out
        Ignored:    slurm-50628144.out
        Ignored:    slurm-50628152.out
        Ignored:    slurm-50628159.out
        Ignored:    slurm-50628168.out
        Ignored:    slurm-50628176.out
        Ignored:    slurm-50628184.out
        Ignored:    slurm-50628189.out
        Ignored:    slurm-50628191.out
        Ignored:    slurm-50628196.out
        Ignored:    slurm-50628199.out
        Ignored:    slurm-50628201.out
        Ignored:    slurm-50628204.out
        Ignored:    slurm-50628207.out
        Ignored:    slurm-50628212.out
        Ignored:    slurm-50628221.out
        Ignored:    slurm-50628226.out
        Ignored:    slurm-50628227.out
        Ignored:    slurm-50628232.out
        Ignored:    slurm-50628240.out
        Ignored:    slurm-50628249.out
        Ignored:    slurm-50628257.out
        Ignored:    slurm-50628264.out
        Ignored:    slurm-50628273.out
        Ignored:    slurm-50628280.out
        Ignored:    slurm-50628289.out
        Ignored:    slurm-50628297.out
        Ignored:    slurm-50628305.out
        Ignored:    slurm-50628311.out
        Ignored:    slurm-50628320.out
        Ignored:    slurm-50628328.out
        Ignored:    slurm-50628336.out
        Ignored:    slurm-50628344.out
        Ignored:    slurm-50628348.out
        Ignored:    slurm-50628353.out
        Ignored:    slurm-50628357.out
        Ignored:    slurm-50628358.out
        Ignored:    slurm-50628359.out
        Ignored:    slurm-50628361.out
        Ignored:    slurm-50628364.out
        Ignored:    slurm-50628366.out
        Ignored:    slurm-50628369.out
        Ignored:    slurm-50628374.out
        Ignored:    slurm-50628377.out
        Ignored:    slurm-50628382.out
        Ignored:    slurm-50628387.out
        Ignored:    slurm-50628396.out
        Ignored:    slurm-50628400.out
        Ignored:    slurm-50628408.out
        Ignored:    slurm-50628416.out
        Ignored:    slurm-50628425.out
        Ignored:    slurm-50628434.out
        Ignored:    slurm-50628443.out
        Ignored:    slurm-50628451.out
        Ignored:    slurm-50628460.out
        Ignored:    slurm-50628469.out
        Ignored:    slurm-50628477.out
        Ignored:    slurm-50628485.out
        Ignored:    slurm-50628493.out
        Ignored:    slurm-50628501.out
        Ignored:    slurm-50628508.out
        Ignored:    slurm-50628514.out
        Ignored:    slurm-50628516.out
        Ignored:    slurm-50628519.out
        Ignored:    slurm-50628522.out
        Ignored:    slurm-50628523.out
        Ignored:    slurm-50628527.out
        Ignored:    slurm-50628528.out
        Ignored:    slurm-50628534.out
        Ignored:    slurm-50628536.out
        Ignored:    slurm-50628537.out
        Ignored:    slurm-50628539.out
        Ignored:    slurm-50628541.out
        Ignored:    slurm-50628543.out
        Ignored:    slurm-50628545.out
        Ignored:    slurm-50628547.out
        Ignored:    slurm-50628548.out
        Ignored:    slurm-50628550.out
        Ignored:    slurm-50628552.out
        Ignored:    slurm-50628554.out
        Ignored:    slurm-50628556.out
        Ignored:    slurm-50628557.out
        Ignored:    slurm-50628559.out
        Ignored:    slurm-50628561.out
        Ignored:    slurm-50628563.out
        Ignored:    slurm-50628565.out
        Ignored:    slurm-50628567.out
        Ignored:    slurm-50628569.out
        Ignored:    slurm-50628571.out
        Ignored:    slurm-50628573.out
        Ignored:    slurm-50628576.out
        Ignored:    slurm-50628580.out
        Ignored:    slurm-50628586.out
        Ignored:    slurm-50628593.out
        Ignored:    slurm-50628600.out
        Ignored:    slurm-50628607.out
        Ignored:    slurm-50628616.out
        Ignored:    slurm-50628621.out
        Ignored:    slurm-50628623.out
        Ignored:    slurm-50628631.out
        Ignored:    slurm-50628637.out
        Ignored:    slurm-50628653.out
        Ignored:    slurm-50628677.out
        Ignored:    slurm-50628701.out
        Ignored:    slurm-50628704.out
        Ignored:    slurm-50628712.out
        Ignored:    slurm-50628723.out
        Ignored:    slurm-50628737.out
        Ignored:    slurm-50628751.out
        Ignored:    slurm-50628761.out
        Ignored:    slurm-50628771.out
        Ignored:    slurm-50628782.out
        Ignored:    slurm-50628794.out
        Ignored:    slurm-50628805.out
        Ignored:    slurm-50628817.out
        Ignored:    slurm-50628827.out
        Ignored:    slurm-50628829.out
        Ignored:    slurm-50628841.out
        Ignored:    slurm-50628855.out
        Ignored:    slurm-50628867.out
        Ignored:    slurm-50628872.out
        Ignored:    slurm-50628874.out
        Ignored:    slurm-50628878.out
        Ignored:    slurm-50628882.out
        Ignored:    slurm-50628885.out
        Ignored:    slurm-50628895.out
        Ignored:    slurm-50628908.out
        Ignored:    slurm-50628917.out
        Ignored:    slurm-50628925.out
        Ignored:    slurm-50628936.out
        Ignored:    slurm-50628950.out
        Ignored:    slurm-50628959.out
        Ignored:    slurm-50628961.out
        Ignored:    slurm-50628970.out
        Ignored:    slurm-50628981.out
        Ignored:    slurm-50628989.out
        Ignored:    slurm-50629001.out
        Ignored:    slurm-50629009.out
        Ignored:    slurm-50629020.out
        Ignored:    slurm-50629030.out
        Ignored:    slurm-50629043.out
        Ignored:    slurm-50629055.out
        Ignored:    slurm-50629064.out
        Ignored:    slurm-50629076.out
        Ignored:    slurm-50629086.out
        Ignored:    slurm-50629088.out
        Ignored:    slurm-50629089.out
        Ignored:    slurm-50629091.out
        Ignored:    slurm-50629093.out
        Ignored:    slurm-50629095.out
        Ignored:    slurm-50629096.out
        Ignored:    slurm-50629098.out
        Ignored:    slurm-50629099.out
        Ignored:    slurm-50629103.out
        Ignored:    slurm-50629104.out
        Ignored:    slurm-50629106.out
        Ignored:    slurm-50629108.out
        Ignored:    slurm-50629110.out
        Ignored:    slurm-50629112.out
        Ignored:    slurm-50629115.out
        Ignored:    slurm-50629117.out
        Ignored:    slurm-50629118.out
        Ignored:    slurm-50629120.out
        Ignored:    slurm-50629122.out
        Ignored:    slurm-50629124.out
        Ignored:    slurm-50629126.out
        Ignored:    slurm-50629128.out
        Ignored:    slurm-50629129.out
        Ignored:    slurm-50629131.out
        Ignored:    slurm-50629133.out
        Ignored:    slurm-50629135.out
        Ignored:    slurm-50629137.out
        Ignored:    slurm-50629138.out
        Ignored:    slurm-50629140.out
        Ignored:    slurm-50629142.out
        Ignored:    slurm-50629144.out
        Ignored:    slurm-50629146.out
        Ignored:    slurm-50629148.out
        Ignored:    slurm-50629150.out
        Ignored:    slurm-50629152.out
        Ignored:    slurm-50629154.out
        Ignored:    slurm-50629156.out
        Ignored:    slurm-50629157.out
        Ignored:    slurm-50629158.out
        Ignored:    slurm-50629160.out
        Ignored:    slurm-50629162.out
        Ignored:    slurm-50629164.out
        Ignored:    slurm-50629166.out
        Ignored:    slurm-50629171.out
        Ignored:    slurm-50629176.out
        Ignored:    slurm-50629186.out
        Ignored:    slurm-50629196.out
        Ignored:    slurm-50629206.out
        Ignored:    slurm-50629209.out
        Ignored:    slurm-50629215.out
        Ignored:    slurm-50629220.out
        Ignored:    slurm-50629224.out
        Ignored:    slurm-50629227.out
        Ignored:    slurm-50629229.out
        Ignored:    slurm-50629233.out
        Ignored:    slurm-50629237.out
        Ignored:    slurm-50629240.out
        Ignored:    slurm-50629243.out
        Ignored:    slurm-50629246.out
        Ignored:    slurm-50629249.out
        Ignored:    slurm-50629252.out
        Ignored:    slurm-50629253.out
        Ignored:    slurm-50629256.out
        Ignored:    slurm-50629259.out
        Ignored:    slurm-50629262.out
        Ignored:    slurm-50629265.out
        Ignored:    slurm-50629268.out
        Ignored:    slurm-50629270.out
        Ignored:    slurm-50629272.out
        Ignored:    slurm-50629274.out
        Ignored:    slurm-50629277.out
        Ignored:    slurm-50629280.out
        Ignored:    slurm-50629283.out
        Ignored:    slurm-50629284.out
        Ignored:    slurm-50629286.out
        Ignored:    slurm-50629289.out
        Ignored:    slurm-50629292.out
        Ignored:    slurm-50629295.out
        Ignored:    slurm-50629298.out
        Ignored:    slurm-50629300.out
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        Ignored:    slurm-50629312.out
        Ignored:    slurm-50629314.out
        Ignored:    slurm-50629316.out
        Ignored:    slurm-50629319.out
        Ignored:    slurm-50629322.out
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        Ignored:    slurm-50629331.out
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        Ignored:    slurm-50629338.out
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        Ignored:    slurm-50629410.out
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        Ignored:    slurm-50629414.out
        Ignored:    slurm-50629415.out
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    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
    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"))
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

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      

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      



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