example/4_make_other_objects.R

In kazeera/hourglass: This Package Provides Visualizations of Annotated Numeric Data

# Continue from 3
library(openxlsx)

# Reformat - make in Format: Stain.Parameter
load("ExampleData2/example_IHC_samples_dataset.RData")
ds <- example_IHC_samples_dataset
colnames(ds$vals)
ds$colAnn$Parameter <- gsub("\\.", "_", ds$colAnn$Parameter)
rownames(ds$colAnn) <- colnames(ds$vals) <- paste(ds$colAnn$Feature, ds$colAnn$Parameter, sep=".")
example_IHC_samples_dataset <- ds

# Save to file
for(ft in names(ds)){
  # save appropriate filetype (ft)
  write.csv(ds[[ft]], file = sprintf("ExampleData2/Example_IHC_sample_%s.csv",ft))
}

# Save R data files
save(example_IHC_samples_dataset, file="ExampleData2/example_IHC_samples_run.RData")

# Make a new list for other tables
example_IHC_samples_run <- list()

# Make a new list element for each sheet for the hourglass template
user_excel <- "Example_IHC_sample_UserOptions.xlsx" #from interface
for(sheet in getSheetNames(user_excel)){
  example_IHC_samples_run[[sheet]] <- read.xlsx(user_excel, sheet = sheet)
}

# Add info
info_excel <- "Example_IHC_sample_Information.xlsx" #from interface
for(sheet in getSheetNames(info_excel)){
  example_IHC_samples_run[[sheet]] <- read.xlsx(info_excel, sheet = sheet)
}

# Save R data files
save(example_IHC_samples_run, file="ExampleData2/example_IHC_samples_run.RData")

# Other inbuilt objects
PANC_TISS_ORDER <- c("reactive","intermediary","deserted")
save(PANC_TISS_ORDER, file="PANC_TISS_ORDER.RData")

# Custom column levels - quantiles
LEVELS <- list(l="low", i="intermed", h="high")
save(LEVELS, file="LEVELS.RData")