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06_clean_NAc_2021.R
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library("SingleCellExperiment")
library("rafalib")
library("iSEE")
library("lobstr")
library("here")
library("whisker")
library("usethis")
library("withr")
library("rsconnect")
library("sessioninfo")
load(here("rdas", "revision", "regionSpecific_NAc-n8_cleaned-combined_MNT2021.rda"), verbose = TRUE)
source(here("shiny_apps", "00_clean_functions.R"))
explore_sce_original(sce.nac)
# [1] "Dimensions:"
# [1] 33538 20571
# [1] "Number of unique cell names:"
# [1] 20514
# [1] "Repeated cell names:"
#
# AAAGAACAGCGAGTCA-1 AAAGGTAGTTTCGTTT-1 AAAGTCCCAGCCTACG-1 AAATGGATCCCGTAAA-1
# 2 2 2 2
# AACACACGTGTGACCC-1 AAGTCGTAGTGGCAGT-1 ACCAACATCGGTCATA-1 ACGATGTGTAGTAAGT-1
# 2 2 2 2
# ACTGCAACAACATCGT-1 AGAAATGCACTTCCTG-1 AGCATCAGTCAAGTTC-1 AGGACTTTCTAGCAAC-1
# 2 2 2 2
# AGGCCACGTCCAGCAC-1 ATCAGGTTCATTCCTA-1 ATGACCAGTTAAGGAT-1 ATGAGGGCAGCTTTGA-1
# 2 2 2 2
# ATGAGTCTCGACATCA-1 ATTACCTAGACTCGAG-1 ATTGGGTTCCGTATAG-1 CACGGGTGTGAGCAGT-1
# 2 2 2 2
# CACTGTCGTCCTTTGC-1 CAGATACGTTGGCCGT-1 CAGGGCTTCAGACCCG-1 CAGTTCCAGTCGTTAC-1
# 2 2 2 2
# CATTCATGTCCTACGG-1 CCCTCAAAGCAATTCC-1 CCGTTCAGTCCATAGT-1 CCTCTCCGTTCAAGTC-1
# 2 2 2 2
# CCTGCATAGTGCTAGG-1 CGTTGGGTCTGTGCAA-1 CTATAGGTCACTGCTC-1 CTCACTGTCGCGTGCA-1
# 2 2 2 2
# CTCTCGACAGTTAAAG-1 GACCGTGGTTGTCTAG-1 GACCTTCGTCTGTAAC-1 GACTGATGTCCGATCG-1
# 2 2 2 2
# GATTTCTAGTGGCGAT-1 GCAGTTAAGTAAGACT-1 GCGTGCAGTATATGGA-1 GGACGTCCAGGTGACA-1
# 2 2 2 2
# GGCTTGGCATCGTGGC-1 GGGTTATGTGCGAGTA-1 GGTGATTAGCTGACAG-1 GTTCCGTGTTGGAGAC-1
# 2 2 2 2
# TAAGCACAGTCATGAA-1 TCACAAGAGGCTTAGG-1 TCCTAATTCGATAACC-1 TCGCAGGTCCGTTTCG-1
# 2 2 2 2
# TGAACGTGTGTCCTAA-1 TGATCAGGTAGGATAT-1 TGCTCGTTCCGCGAGT-1 TGGAACTGTGGTTCTA-1
# 2 2 2 2
# TGGGAAGAGAAGGGAT-1 TGGGATTGTGATGAAT-1 TGTGTGACACTGTGAT-1 TTGACCCGTTCCGCTT-1
# 2 2 2 2
# TTGTGTTCAATCGCGC-1
# 2
# [1] "Number of unique genes names:"
# [1] 33538
sce_small <- create_small_sce_2021(sce.nac)
# * 2.120966 B
# * 1.093446 B
dim(sce_small)
# [1] 33538 19892
colData(sce_small)
rowData(sce_small)
## Test and get the "initial" code
# iSEE(sce_small)
save_sce_small(sce_small, "NAc", prefix = "tran2021_")
save_cell_colors(cell_colors.nac, "NAc")
create_app(sce_small, "NAc", cellmarkers = cellmarkers_fig_s7_2021, prefix = "tran2021_")
withr::with_dir(here("shiny_apps", "tran2021_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 4.1.0 (2021-05-18)
# os macOS Big Sur 11.4
# system x86_64, darwin17.0
# ui RStudio
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz America/New_York
# date 2021-07-27
#
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