diff --git a/inst/scripts/multivar_mine.R b/inst/scripts/multivar_mine.R
index dc3efe6..0154b30 100755
--- a/inst/scripts/multivar_mine.R
+++ b/inst/scripts/multivar_mine.R
@@ -15,18 +15,21 @@ if( Sys.getenv('DEGHUNTER_MODE') == 'DEVELOPMENT' ){
root_path <- file.path(main_path_script, '..', '..')
# Load custom libraries
custom_libraries <- list.files(file.path(root_path, "R"), full.names = TRUE)
+ # template_folder <- file.path(root_path, 'inst/templates')
+ template_folder <- file.path(root_path, 'inst/templates', 'htmlreport_migration')
invisible(sapply(custom_libraries, source)) # source(file.path(root_path, 'R', lib))
- template_folder <- file.path(root_path, 'inst', 'templates')
}else{
require('ExpHunterSuite')
root_path <- find.package('ExpHunterSuite')
- template_folder <- file.path(root_path, 'templates')
+ # template_folder <- file.path(root_path, 'templates')
+ template_folder <- file.path(root_path, 'templates', 'htmlreport_migration')
}
+
# Prepare command line input
option_list <- list(
optparse::make_option(c("-i", "--input_file"), type="character", default=NULL,
@@ -43,10 +46,10 @@ option_list <- list(
optparse::make_option(c("-t", "--transpose"), type="logical", action = "store_true",
default=FALSE,
help="If activated, rows are treated as variables and columns as samples."),
- optparse::make_option(c("-S", "--add_cualitative_vars"), type="character",
+ optparse::make_option(c("-S", "--add_qualitative_vars"), type="character",
default=NULL,
help="Variables in the input to be treated as supplementary QUALITATIVE variables"),
- optparse::make_option(c("-N", "--add_cuantitative_vars"), type="character",
+ optparse::make_option(c("-N", "--add_quantitative_vars"), type="character",
default=NULL,
help="Variables in the input to be treated as supplementary QUANTITATIVE variables"),
optparse::make_option(c("-s", "--add_samples"), type="character",
@@ -58,12 +61,12 @@ opt <- optparse::parse_args(optparse::OptionParser(option_list=option_list))
input_file <- read.table(file.path(opt$input_file), header = TRUE, row.names = 1)
-if (!is.null(opt$add_cuantitative_vars)) {
- opt$add_cuantitative_vars <- split_str(opt$add_cuantitative_vars, ",")
+if (!is.null(opt$add_quantitative_vars)) {
+ opt$add_quantitative_vars <- split_str(opt$add_quantitative_vars, ",")
}
-if (!is.null(opt$add_cualitative_vars)) {
- opt$add_cualitative_vars <- split_str(opt$add_cualitative_vars, ",")
+if (!is.null(opt$add_qualitative_vars)) {
+ opt$add_qualitative_vars <- split_str(opt$add_qualitative_vars, ",")
}
if (!is.null(opt$add_samples)) {
@@ -76,16 +79,30 @@ if(!file.exists(opt$output_files))
if (opt$analysis_type == "pca") {
pca_res <- compute_pca(pca_data = input_file,
transpose = opt$transpose,
- string_factors = opt$add_cualitative_vars,
- numeric_factors = opt$add_cuantitative_vars,
+ string_factors = opt$add_qualitative_vars,
+ numeric_factors = opt$add_quantitative_vars,
add_samples = opt$add_samples)
pca_output <- file.path(opt$output_files, "PCA_results")
dir.create(pca_output)
write_general_pca(pca_res, pca_output)
- rmarkdown::render(input = file.path(template_folder, 'main_PCA.Rmd'),
- intermediates_dir = file.path(opt$output_files, "tmp"),
- output_file = file.path(opt$output_files, "PCA_report.html"))
+ devtools::load_all("/mnt/home/users/bio_267_uma/josecordoba/software/htmlreportR")
+ source_folder <- find.package('htmlreportR')
+
+ if( Sys.getenv('HTMLREPORTER_MODE') == 'DEVELOPMENT' )
+ source_folder <- file.path(source_folder, "inst")
+
+ pca_res$string_factors <-opt$add_qualitative_vars
+ pca_res$numeric_factors <- opt$add_quantitative_vars
+ plotter <- htmlReport$new(title_doc = "PCA report",
+ container = pca_res,
+ tmp_folder = file.path(opt$output_files, "tmp"),
+ src = source_folder,
+ compress_obj = FALSE,
+ type_index = "menu")
+
+ plotter$build(file.path(template_folder, 'main_PCA.txt'))
+ plotter$write_report(file.path(opt$output_files, "PCA_report.html"))
}
\ No newline at end of file
diff --git a/inst/templates/htmlreport_migration/facto_miner.txt b/inst/templates/htmlreport_migration/facto_miner.txt
new file mode 100644
index 0000000..27cbda6
--- /dev/null
+++ b/inst/templates/htmlreport_migration/facto_miner.txt
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\ No newline at end of file
diff --git a/inst/templates/htmlreport_migration/main_PCA.txt b/inst/templates/htmlreport_migration/main_PCA.txt
new file mode 100644
index 0000000..c5f6a37
--- /dev/null
+++ b/inst/templates/htmlreport_migration/main_PCA.txt
@@ -0,0 +1,30 @@
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