Sequencing depth per C1 chip
John Blischak
2017-11-28
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 runwflow_publishto 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.
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✔ 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.
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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.✔ Repository version: b467002
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 usewflow_publishorwflow_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:
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.Ignored files: Ignored: .Rhistory Ignored: .Rproj.user/ Ignored: .snakemake/ Ignored: data/molecules/ Ignored: data/reads/ Ignored: data/totals/ Ignored: data/verify/ Ignored: log/ Ignored: slurm-46031744.out Ignored: slurm-50622757.out Ignored: slurm-50622948.out Ignored: slurm-50622950.out Ignored: slurm-50622951.out Ignored: slurm-50622954.out Ignored: slurm-50622956.out Ignored: slurm-50622998.out Ignored: slurm-50623000.out Ignored: slurm-50623005.out Ignored: slurm-50623025.out Ignored: slurm-50623028.out Ignored: slurm-50623029.out Ignored: slurm-50623031.out Ignored: slurm-50623033.out Ignored: slurm-50623035.out Ignored: slurm-50623037.out Ignored: slurm-50623038.out Ignored: slurm-50623040.out Ignored: slurm-50623043.out Ignored: slurm-50623045.out Ignored: slurm-50623047.out Ignored: slurm-50623048.out Ignored: 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analysis/_site.yml Modified: analysis/about.Rmd Modified: analysis/cellcycler-seqdata-leng.Rmd Deleted: analysis/chunks.R Modified: analysis/circ-simulation-correlation.Rmd Modified: analysis/confess-prelim.Rmd Modified: analysis/ensembl.Rmd Modified: analysis/gene-filtering.Rmd Modified: analysis/images-cellcycleR-convergence.Rmd Modified: analysis/images-cellcycleR.Rmd Modified: analysis/images-circle-ordering-eval.Rmd Modified: analysis/images-circle-ordering-sigcorgenes.Rmd Modified: analysis/images-circle-ordering.Rmd Modified: analysis/images-classify-fucci-adjusted.Rmd Modified: analysis/images-classify-fucci.Rmd Modified: analysis/images-classify-leng.Rmd Modified: analysis/images-mclust.Rmd Modified: analysis/images-metrics-cell-shape.Rmd Modified: analysis/images-metrics.Rmd Modified: analysis/images-multiple-nuclei.Rmd Modified: analysis/images-normalize-anova.Rmd Modified: analysis/images-normalize-quantile.Rmd Modified: analysis/images-pam.Rmd Modified: analysis/images-process.Rmd Modified: analysis/images-qc-followup.Rmd Modified: analysis/images-qc-labels.Rmd Modified: analysis/images-qc-variation.Rmd Modified: analysis/images-qc.Rmd Modified: analysis/images-seq-correlation.Rmd Modified: analysis/images-subset-silhouette.Rmd Modified: analysis/images-time-eval.Rmd Modified: analysis/images-transgene.Rmd Modified: analysis/images-zero-nuclei.Rmd Modified: analysis/index.Rmd Modified: analysis/license.Rmd Modified: analysis/method-eval-withheld-explore-removenoisy.Rmd Modified: analysis/method-eval-withheld-explore.Rmd Modified: analysis/method-eval.Rmd Modified: analysis/method-labels-compare.Rmd Modified: analysis/method-labels-noisy.Rmd Modified: analysis/method-labels-seurat.Rmd Modified: analysis/method-labels.Rmd Modified: analysis/method-npreg-prelim-results.Rmd Modified: analysis/method-npreg.Rmd Modified: analysis/method-spml.Rmd Modified: analysis/method-train-alge.Rmd Modified: analysis/method-train-classifiers-all.Rmd 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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
This reproducible R Markdown analysis was created with workflowr 1.0.1