add r temporaries to gitignore

.gitignore

@@ -382,3 +382,7 @@ Network Trash Folder
 Temporary Items
 .apdisk
 
+
+# R temporaries
+.Rhistory
+.RData

workflows/.Rhistory

-# ### sleuth installation
-#
-if (!requireNamespace("BiocManager", quietly = TRUE))
-install.packages("BiocManager")
-if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
-BiocManager::install()
-BiocManager::install("devtools")    # only if devtools not yet installed
-BiocManager::install("pachterlab/sleuth")
-library(sleuth)
-BiocManager::install("pachterlab/sleuth")
-library(sleuth)
-BiocManager::install("pachterlab/sleuth")
-install.packages('Matrix', dependencies = TRUE)
-BiocManager::install("pachterlab/sleuth")
-source("http://bioconductor.org/biocLite.R")
-devtools::install_github("pachterlab/sleuth")
-remotes::install_github("pachterlab/sleuth#260")
-library(sleuth)
-# BiocManager::install("pachterlab/sleuth")
-# There's currently (early 2022) an issue with sleuth installation.
-# Using this workaround from https://github.com/pachterlab/sleuth/issues/259#issuecomment-1001076030
-remotes::install_github("pachterlab/sleuth#260")
-library(sleuth)
-library(tidyverse)
-library(jsonlite)
-library(openxlsx)
-?commandArgs
-BiocManager::install()
-library(sleuth)
-required_packages <-
-c('tidyverse',  ## data wrangling and plotting
-'jsonlite',   ## read/write json files
-'openxlsx')   ## read/write xlsx files
-for(package in required_packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package,
-repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-}
-for(package in required_packages)
-{
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package,
-repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-print(paste(package, "installed"))
-}
-{
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package,
-repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-print(paste("installed R package", package))
-}
-for(package in required_packages)
-{
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages())){install.packages(package,
-repos ="https://cran.uni-muenster.de/")}
-# ## Check if package is up to date. If not, update
-# update.packages(package, repos = "https://cran.uni-muenster.de/")
-## Load package
-library(package, character.only = T)
-print(paste("installed R package", package))
-}
-run_name="run1"
-arc_root="~/03DataPLANT_gitlab/samplearc_rnaseq/"
-# Load the sleuth object
-load(file = paste0(arc_root, 'runs/', run_name, '/03_kallisto_sleuthObject.RData'))
-so <- sleuth_fit(so)
-so <- sleuth_fit(so, ~Group, 'full')
-so <- sleuth_fit(so, ~Photosynthesis.mode, 'full')
-so <- sleuth_fit(so, ~1, 'reduced')
-so <- sleuth_lrt(so, 'reduced', 'full')
-sleuth_table <- sleuth_results(so, 'reduced:full', 'lrt', show_all = FALSE)
-write.csv(sleuth_table, paste0(arc_root, 'runs/', run_name, '/04_sleuth_dge.csv'), row.names = F)
-library(openxlsx)
-expression_data <- read.csv(file = paste0(arc_root, 'runs/', run_name, '/03_kallisto_df.csv'))
-available_genes <- unique(expression_data$target_id)
-save(expression_data, available_genes, file = paste0(arc_root, 'runs/', run_name, '/05_shinyPrep.RData'))
-load(file = "../runs/run1/05_shinyPrep.RData")
-required.packages <- c('knitr', 'kableExtra', ## RMarkdown,
-"shiny", "tidyverse", ## data loading and shaping
-"RColorBrewer", "shiny" ## plotting
-)
-for(package in required.packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages()))
-{install.packages(package, repos ="https://cran.uni-muenster.de/")}
-## Load package
-library(package, character.only = T)
-}
-required.packages <- c('kableExtra', ## RMarkdown,
-"shiny", "tidyverse", ## data loading and shaping
-"RColorBrewer", "shiny" ## plotting
-)
-for(package in required.packages)
-{
-print(package)
-## Check if package is installed. If not, install
-if(!package %in% row.names(installed.packages()))
-{install.packages(package, repos ="https://cran.uni-muenster.de/")}
-## Load package
-library(package, character.only = T)
-}
-current_selection <- sample(expression_data$target_id, 10)
-plot_set <- subset(expression_data, target_id %in% current_selection)
-ggplot(plot_set, aes(x = Group, y = tpm, group = Group)) +
-stat_summary(fun = 'mean', geom = 'bar') +
-geom_point(size = 0.5) +
-facet_wrap(~ target_id , scales = "free") +
-theme_minimal()
-plot_set <- subset(expression_data, target_id %in% current_selection)
-ggplot(plot_set, aes(x = Photosynthesis.mode, y = tpm, group = Photosynthesis.mode)) +
-stat_summary(fun = 'mean', geom = 'bar') +
-geom_point(size = 0.5) +
-facet_wrap(~ target_id , scales = "free") +
-theme_minimal()