lcolladotor

# Bad examples from https://style.tidyverse.org/syntax.html
x[,1]
x[ ,1]
x[ , 1]

# Bad
mean (x, na.rm = TRUE)
mean( x, na.rm = TRUE )

# Bad

lcolladotor

library("tidyverse")
library("here")
chocolate <- readRDS(here("data", "chocolate.RDS"))

## Base R solution
has_sugar <- sapply(
    strsplit(
        gsub(" ", "", gsub(".*-", "", chocolate$ingredients)),
        ","),
    function(x) { any(x == "S") }

lcolladotor

library("tidyverse")
library("here")
chocolate <- readRDS(here("data", "chocolate.RDS"))
glimpse(chocolate)

options(width = 120)
sessioninfo::session_info()

## After copying the above, I ran:
# reprex::reprex(wd = here::here())

lcolladotor

## R 4.3.2 bioc 3.18 test

```R
> library("recount3")
> args(recount3_cache)
function (cache_dir = getOption("recount3_cache", NULL))
NULL
> rse_data <- recount3::create_rse_manual(
+   project = "SRP045225",
+   project_home = "data_sources/sra",

lcolladotor

library("dplyr")
library("sessioninfo")

tuesdata <- tidytuesdayR::tt_load("2020-01-07")
rainfall <- tuesdata$rainfall

rainfall_filtered <- rainfall %>% 
    filter(city_name == "Cuernavaca")

rainfall_filtered

lcolladotor

x <- c("/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-04-19-latin-american-r-bioconductor-developers-workshop-2018.html:44:1",
"/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-06-11-mindfulness.html:27:1",
"/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-07-30-harrassment-diversity-in-science-and-inspiraton-from-my-grandmother.html:24:1",
"/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-09-13-r-gene-regulatory-interaction-formulator-for-inquiring-networks.html:132:1",
"/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-09-17-what-about-a-lawyer-like-app-as-the-mininum-help-for-defandants-in-immigration-cases.html:110:1",
"/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-10-16-ashg18-tweet-summary.html:21:1",
"/Users/leocollado/Dropbox/Code/lcolladotorsource/content/post/2018-09-29-why-i-applied-to-join-sni-the-mexican-national-researchers-registry.html:21:1",
"/Users/leocollado/Dropbox/Code/lcollado

lcolladotor

## Load required libraries
library("googlesheets4")
library("dplyr")
library("ggplot2")
library("plotly")
## For reproducibility
library("sessioninfo")

## Authenticate with Google
googlesheets4::gs4_auth()

lcolladotor

library('SpatialExperiment')
library('ggplot2')
library('gridExtra')
library('ggspavis')

id = 'V10B01-085_A1'
spe_path = '/dcs04/lieber/lcolladotor/spatialHPC_LIBD4035/spatial_hpc/processed-data/pilot_data_checks/spe_basic.Rdata'

################################################################################
#   Function Definitions

lcolladotor

"","Sample.ID","Number.of.Reads","Mean.Reads.per.Spot","Median.Genes.per.Spot","Median.UMI.Counts.per.Spot","Valid.Barcodes","Sequencing.Saturation","Q30.Bases.in.Barcode","Q30.Bases.in.RNA.Read","Q30.Bases.in.UMI","Reads.Mapped.to.Genome","Reads.Mapped.Confidently.to.Genome","Reads.Mapped.Confidently.to.Intergenic.Regions","Reads.Mapped.Confidently.to.Intronic.Regions","Reads.Mapped.Confidently.to.Exonic.Regions","Reads.Mapped.Confidently.to.Transcriptome","Reads.Mapped.Antisense.to.Gene","Total.Genes.Detected","study"
"1","V10A27004_A1_Br3874",250388898,50995.7022403259,1302,2348,96.1,91.9,96.2,93.9,95.8,95.1,79.8,8.7,2.3,68.7,66.4,1,22439,"VisiumIF"
"2","V10A27004_D1_Br3880",173548606,37646.1184381779,1155,2058,95.6,89.5,96.4,93.8,95.8,95.2,74.3,5.8,2.7,65.8,62.9,1.5,22355,"VisiumIF"
"3","V10A27106_A1_Br3874",316562059,75605.9371865297,1347,2176,96.7,93.6,96.3,94,95.7,95,78.1,10.3,4.4,63.3,61.6,0.6,22809,"VisiumIF"
"4","V10A27106_B1_Br3854",204558515,76157.3026805659,1126.5,1938,96.6,94,96.4,94.5,95.8,96.9

lcolladotor

cd /dcl01/lieber/ajaffe/lab
# cd ~ # My tests didn't work in my home dir (setfacl: test_main: Operation not supported)
mkdir test_setfacl
cd test_setfacl
rm -fr test_main test_proj2


mkdir test_main
chgrp lieber_jaffe test_main
chmod g+s test_main