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01_clean_NAc.R
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library("SingleCellExperiment")
library("rafalib")
library("iSEE")
library("pryr")
library("here")
library("whisker")
library("usethis")
library("withr")
library("sessioninfo")
load(here("rdas", "ztemp_NAc-ALL-n5_SCE-with-tSNEon15-10PCs_MNT.rda"), verbose = TRUE)
source(here("shiny_apps", "00_clean_functions.R"))
explore_sce_original(sce.all.tsne.15pcs)
# [1] "Dimensions:"
# [1] 33538 13148
# [1] "Number of unique cell names:"
# [1] 13131
# [1] "Repeated cell names:"
#
# AGAAATGCACTTCCTG-1 AGGACTTTCTAGCAAC-1 ATGAGTCTCGACATCA-1 CACGGGTGTGAGCAGT-1 CATTCATGTCCTACGG-1
# 2 2 2 2 2
# CCGTTCAGTCCATAGT-1 CTATAGGTCACTGCTC-1 CTCTCGACAGTTAAAG-1 GACCGTGGTTGTCTAG-1 GACTGATGTCCGATCG-1
# 2 2 2 2 2
# GATTTCTAGTGGCGAT-1 GCAGTTAAGTAAGACT-1 GGGTTATGTGCGAGTA-1 TAAGCACAGTCATGAA-1 TCGCAGGTCCGTTTCG-1
# 2 2 2 2 2
# TGATCAGGTAGGATAT-1 TGGGATTGTGATGAAT-1
# 2 2
# [1] "Number of unique genes names:"
# [1] 33538
sce_small <- create_small_sce(sce.all.tsne.15pcs)
# 1.55 GB
# 801 MB
colData(sce_small)
rowData(sce_small)
## Test and get the "initial" code
# iSEE(sce_small)
save_sce_small(sce_small, "NAc")
create_app(sce_small, "NAc")
withr::with_dir(here("shiny_apps", "tran2020_NAc"), source("deploy.R"))
## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
# - Session info -------------------------------------------------------------------------------------------------------
# setting value
# version R version 4.0.2 (2020-06-22)
# os Windows 10 x64
# system x86_64, mingw32
# ui RStudio
# language (EN)
# collate English_United States.1252
# ctype English_United States.1252
# tz America/New_York
# date 2020-09-28
#
# - Packages -----------------------------------------------------------------------------------------------------------
# package * version date lib source
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# circlize 0.4.10 2020-06-15 [1] CRAN (R 4.0.2)
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# clue 0.3-57 2019-02-25 [1] CRAN (R 4.0.2)
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# fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
# generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2)
# GenomeInfoDb * 1.24.2 2020-06-15 [1] Bioconductor
# GenomeInfoDbData 1.2.3 2020-06-30 [1] Bioconductor
# GenomicRanges * 1.40.0 2020-04-27 [1] Bioconductor
# GetoptLong 1.0.2 2020-07-06 [1] CRAN (R 4.0.2)
# ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
# GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.0.2)
# glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
# gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
# here * 0.1 2017-05-28 [1] CRAN (R 4.0.2)
# htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
# htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.2)
# httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2)
# igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.2)
# IRanges * 2.22.2 2020-05-21 [1] Bioconductor
# iSEE * 2.0.0 2020-04-27 [1] Bioconductor
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# Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
# matrixStats * 0.56.0 2020-03-13 [1] CRAN (R 4.0.2)
# mgcv 1.8-33 2020-08-27 [1] CRAN (R 4.0.2)
# mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
# miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2)
# munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
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# pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
# png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0)
# promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2)
# pryr * 0.1.4 2018-02-18 [1] CRAN (R 4.0.2)
# purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
# R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
# rafalib * 1.0.0 2015-08-09 [1] CRAN (R 4.0.0)
# RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
# Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
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# rjson 0.2.20 2018-06-08 [1] CRAN (R 4.0.0)
# rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
# rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
# rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2)
# S4Vectors * 0.26.1 2020-05-16 [1] Bioconductor
# scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
# shape 1.4.5 2020-09-13 [1] CRAN (R 4.0.2)
# shiny 1.5.0 2020-06-23 [1] CRAN (R 4.0.2)
# shinyAce 0.4.1 2019-09-24 [1] CRAN (R 4.0.2)
# shinydashboard 0.7.1 2018-10-17 [1] CRAN (R 4.0.2)
# shinyjs 2.0.0 2020-09-09 [1] CRAN (R 4.0.2)
# shinyWidgets 0.5.3 2020-06-01 [1] CRAN (R 4.0.2)
# SingleCellExperiment * 1.10.1 2020-04-28 [1] Bioconductor
# stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
# stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
# SummarizedExperiment * 1.18.2 2020-07-09 [1] Bioconductor
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# usethis * 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
# vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
# vipor 0.4.5 2017-03-22 [1] CRAN (R 4.0.2)
# viridisLite 0.3.0 2018-02-01 [1] CRAN (R 4.0.2)
# whisker * 0.4 2019-08-28 [1] CRAN (R 4.0.2)
# withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
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# XVector 0.28.0 2020-04-27 [1] Bioconductor
# zlibbioc 1.34.0 2020-04-27 [1] Bioconductor
#
# [1] D:/R/R-4.0.2/library