@@ -10,3 +10,4 @@

 ^pkgdown$

 ^doc$

 ^Design$

+^sample_reports$

@@ -35,3 +35,6 @@ unsrturl.bst

 inst/doc

 ISAnalytics.Rproj

 docs

+sample_reports

+README.Rmd

+NEWS.Rmd

@@ -1,6 +1,6 @@

 Package: ISAnalytics

 Title: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

-Version: 1.3.2

+Version: 1.3.3

 Date: 2020-07-03

 Authors@R: c(

   person(given = "Andrea",

@@ -25,8 +25,6 @@ Depends:

     magrittr

 Imports: 

     utils,

-    reactable,

-    htmltools,

     dplyr,

     readr,

     tidyr,

@@ -36,20 +34,18 @@ Imports:

     BiocParallel,

     stringr,

     fs,

-    zip,

     lubridate,

     lifecycle,

     ggplot2,

     ggrepel,

     stats,

-    upsetjs,

     psych,

-    grDevices,

     data.table,

     readxl,

     tools,

     Rcapture,

-    plotly

+    grDevices, 

+    zip

 Encoding: UTF-8

 LazyData: false

 Roxygen: list(markdown = TRUE)

@@ -59,7 +55,6 @@ Suggests:

     covr,

     knitr,

     BiocStyle,

-    knitcitations,

     sessioninfo,

     rmarkdown,

     roxygen2,

@@ -69,7 +64,13 @@ Suggests:

     ggalluvial,

     scales,

     gridExtra,

-    R.utils

+    R.utils,

+    RefManageR,

+    flexdashboard,

+    DT,

+    circlize,

+    plotly,

+    ggvenn

 VignetteBuilder: knitr

 RdMacros: 

     lifecycle

@@ -11,6 +11,7 @@ export(as_sparse_matrix)

 export(association_file_columns)

 export(available_outlier_tests)

 export(blood_lineages_default)

+export(circos_genomic_density)

 export(clinical_relevant_suspicious_genes)

 export(comparison_matrix)

 export(compute_abundance)

@@ -20,11 +21,13 @@ export(date_columns_coll)

 export(date_formats)

 export(default_iss_file_prefixes)

 export(default_meta_agg)

+export(default_report_path)

 export(default_stats)

 export(generate_Vispa2_launch_AF)

 export(generate_blank_association_file)

 export(import_Vispa2_stats)

 export(import_association_file)

+export(import_parallel_Vispa2Matrices)

 export(import_parallel_Vispa2Matrices_auto)

 export(import_parallel_Vispa2Matrices_interactive)

 export(import_single_Vispa2Matrix)

@@ -38,6 +41,7 @@ export(outliers_by_pool_fragments)

 export(quantification_types)

 export(realign_after_collisions)

 export(reduced_AF_columns)

+export(refGene_table_cols)

 export(remove_collisions)

 export(sample_statistics)

 export(separate_quant_matrices)

@@ -46,12 +50,8 @@ export(threshold_filter)

 export(top_abund_tableGrob)

 export(top_integrations)

 export(unzip_file_system)

-import(BiocParallel)

-import(dplyr)

 import(ggplot2)

-import(htmltools)

 import(lifecycle)

-import(upsetjs)

 importFrom(BiocParallel,MulticoreParam)

 importFrom(BiocParallel,SnowParam)

 importFrom(BiocParallel,bplapply)

@@ -61,28 +61,48 @@ importFrom(BiocParallel,bptry)

 importFrom(Rcapture,closedp.0)

 importFrom(Rcapture,closedp.bc)

 importFrom(data.table,.SD)

+importFrom(data.table,`%chin%`)

 importFrom(data.table,fread)

 importFrom(data.table,melt.data.table)

 importFrom(data.table,rbindlist)

 importFrom(data.table,setDT)

+importFrom(data.table,setnames)

 importFrom(dplyr,across)

 importFrom(dplyr,all_of)

+importFrom(dplyr,anti_join)

 importFrom(dplyr,arrange)

 importFrom(dplyr,bind_cols)

 importFrom(dplyr,bind_rows)

+importFrom(dplyr,contains)

+importFrom(dplyr,cur_column)

+importFrom(dplyr,desc)

 importFrom(dplyr,distinct)

+importFrom(dplyr,everything)

 importFrom(dplyr,filter)

+importFrom(dplyr,first)

 importFrom(dplyr,full_join)

 importFrom(dplyr,group_by)

+importFrom(dplyr,group_keys)

+importFrom(dplyr,group_modify)

 importFrom(dplyr,group_split)

+importFrom(dplyr,if_else)

 importFrom(dplyr,inner_join)

 importFrom(dplyr,intersect)

 importFrom(dplyr,left_join)

 importFrom(dplyr,mutate)

+importFrom(dplyr,n)

+importFrom(dplyr,n_distinct)

+importFrom(dplyr,pull)

 importFrom(dplyr,rename)

+importFrom(dplyr,rename_with)

 importFrom(dplyr,select)

 importFrom(dplyr,semi_join)

 importFrom(dplyr,slice)

+importFrom(dplyr,slice_head)

+importFrom(dplyr,starts_with)

+importFrom(dplyr,summarise)

+importFrom(dplyr,transmute)

+importFrom(dplyr,ungroup)

 importFrom(fs,as_fs_path)

 importFrom(fs,dir_create)

 importFrom(fs,dir_exists)

@@ -92,28 +112,34 @@ importFrom(fs,is_dir)

 importFrom(fs,path)

 importFrom(fs,path_dir)

 importFrom(fs,path_ext)

+importFrom(fs,path_ext_set)

+importFrom(fs,path_home)

 importFrom(fs,path_wd)

+importFrom(ggplot2,aes)

 importFrom(ggplot2,aes_)

+importFrom(ggplot2,element_blank)

+importFrom(ggplot2,element_text)

+importFrom(ggplot2,geom_hline)

+importFrom(ggplot2,geom_point)

+importFrom(ggplot2,geom_raster)

 importFrom(ggplot2,geom_text)

 importFrom(ggplot2,ggplot)

+importFrom(ggplot2,ggplot_build)

+importFrom(ggplot2,labs)

+importFrom(ggplot2,rel)

+importFrom(ggplot2,scale_alpha_continuous)

+importFrom(ggplot2,scale_fill_gradientn)

 importFrom(ggplot2,scale_fill_viridis_d)

+importFrom(ggplot2,scale_x_continuous)

+importFrom(ggplot2,scale_y_continuous)

 importFrom(ggplot2,sym)

+importFrom(ggplot2,theme)

+importFrom(ggplot2,unit)

 importFrom(ggrepel,geom_label_repel)

-importFrom(grDevices,colorRamp)

-importFrom(grDevices,rgb)

-importFrom(htmltools,browsable)

-importFrom(htmltools,div)

-importFrom(htmltools,h1)

-importFrom(htmltools,h2)

-importFrom(htmltools,h3)

-importFrom(htmltools,h4)

-importFrom(htmltools,save_html)

-importFrom(htmltools,tagList)

-importFrom(htmltools,tags)

+importFrom(lifecycle,deprecate_warn)

 importFrom(lubridate,parse_date_time)

+importFrom(lubridate,today)

 importFrom(magrittr,`%>%`)

-importFrom(plotly,plot_ly)

-importFrom(psych,describe)

 importFrom(purrr,cross_df)

 importFrom(purrr,detect_index)

 importFrom(purrr,flatten)

@@ -129,9 +155,11 @@ importFrom(purrr,map2_lgl)

 importFrom(purrr,map_chr)

 importFrom(purrr,map_dbl)

 importFrom(purrr,map_dfr)

+importFrom(purrr,map_int)

 importFrom(purrr,map_lgl)

 importFrom(purrr,pmap)

 importFrom(purrr,pmap_chr)

+importFrom(purrr,pmap_dbl)

 importFrom(purrr,pmap_df)

 importFrom(purrr,pmap_dfr)

 importFrom(purrr,pmap_lgl)

@@ -139,22 +167,18 @@ importFrom(purrr,reduce)

 importFrom(purrr,set_names)

 importFrom(purrr,walk)

 importFrom(purrr,walk2)

-importFrom(reactable,colDef)

-importFrom(reactable,colFormat)

-importFrom(reactable,reactable)

-importFrom(reactable,reactableTheme)

 importFrom(readr,cols)

-importFrom(readr,parse_factor)

 importFrom(readr,problems)

 importFrom(readr,read_delim)

 importFrom(readr,write_tsv)

-importFrom(readxl,read_excel)

 importFrom(rlang,.data)

+importFrom(rlang,`!!!`)

 importFrom(rlang,`:=`)

 importFrom(rlang,abort)

 importFrom(rlang,arg_match)

 importFrom(rlang,as_function)

 importFrom(rlang,call2)

+importFrom(rlang,current_env)

 importFrom(rlang,dots_list)

 importFrom(rlang,enexpr)

 importFrom(rlang,env_bind)

@@ -167,11 +191,9 @@ importFrom(rlang,is_formula)

 importFrom(rlang,is_function)

 importFrom(rlang,list2)

 importFrom(rlang,parse_expr)

+importFrom(rlang,sym)

 importFrom(stats,dt)

-importFrom(stats,median)

 importFrom(stats,na.omit)

-importFrom(stats,p.adjust)

-importFrom(stats,pt)

 importFrom(stats,setNames)

 importFrom(stats,shapiro.test)

 importFrom(stringr,str_detect)

@@ -179,17 +201,14 @@ importFrom(stringr,str_pad)

 importFrom(stringr,str_replace)

 importFrom(stringr,str_replace_all)

 importFrom(stringr,str_split)

+importFrom(stringr,str_to_lower)

 importFrom(stringr,str_to_upper)

+importFrom(tibble,add_case)

 importFrom(tibble,add_column)

-importFrom(tibble,add_row)

 importFrom(tibble,as_tibble)

 importFrom(tibble,as_tibble_col)

-importFrom(tibble,as_tibble_row)

-importFrom(tibble,is_tibble)

 importFrom(tibble,tibble)

-importFrom(tibble,tibble_row)

 importFrom(tibble,tribble)

-importFrom(tidyr,everything)

 importFrom(tidyr,nest)

 importFrom(tidyr,pivot_longer)

 importFrom(tidyr,pivot_wider)

@@ -2,6 +2,45 @@

 title: "NEWS"

 output: github_document

 ---

+# ISAnalytics 1.3.3 (TBD)

+

+## MAJOR CHANGES

+* Completely reworked interactive HTML report system, for details take

+a look at the new vignette `vignette("report_system", package = "ISAnalytics")`

+* Old `ISAnalytics.widgets` option has been replaced by `ISAnalytics.reports`

+* In `remove_collisions()`, removed arguments `seq_count_col`,

+`max_rows_reports` and `save_widget_path`, added arguments `quant_cols`

+and `report_path` (see documentation for details)

+

+## MINOR CHANGES

+* `import_single_Vispa2Matrix()` now allows keeping additional non-standard

+columns

+* `compute_near_integrations()` is now faster on bigger data sets

+* Changed default values for arguments `columns` and `key` in 

+`compute_abundance()`

+* `compute_near_integrations()` now produces only re-calibration map in *.tsv

+format

+* `CIS_grubbs()` now supports calculations for each group specified in argument

+`by`

+* In `sample_statistics()` now there is the option to include the calculation

+of distinct integration sites for each group (if mandatory vars are present)

+

+## NEW FUNCTIONALITY

+* Added new plotting function `circos_genomic_density()`

+

+## FIXES

+* Fixed minor issue with NA values in alluvial plots

+

+## DEPRECATIONS

+* `import_parallel_Vispa2Matrices_interactive()` and

+`import_parallel_Vispa2Matrices_auto()` are officially deprecated in favor

+of `import_parallel_Vispa2Matrices()`

+

+## OTHER

+* The package has now a more complete and functional example data set 

+for executable examples

+* Reworked documentation

+

 # ISAnalytics 1.3.2 (2021-06-28)

 ## FIXES

@@ -1,6 +1,54 @@

 NEWS

 ================

+# ISAnalytics 1.3.3 (TBD)

+

+## MAJOR CHANGES

+

+-   Completely reworked interactive HTML report system, for details take

+    a look at the new vignette

+    `vignette("report_system", package = "ISAnalytics")`

+-   Old `ISAnalytics.widgets` option has been replaced by

+    `ISAnalytics.reports`

+-   In `remove_collisions()`, removed arguments `seq_count_col`,

+    `max_rows_reports` and `save_widget_path`, added arguments

+    `quant_cols` and `report_path` (see documentation for details)

+

+## MINOR CHANGES

+

+-   `import_single_Vispa2Matrix()` now allows keeping additional

+    non-standard columns

+-   `compute_near_integrations()` is now faster on bigger data sets

+-   Changed default values for arguments `columns` and `key` in

+    `compute_abundance()`

+-   `compute_near_integrations()` now produces only re-calibration map

+    in \*.tsv format

+-   `CIS_grubbs()` now supports calculations for each group specified in

+    argument `by`

+-   In `sample_statistics()` now there is the option to include the

+    calculation of distinct integration sites for each group (if

+    mandatory vars are present)

+

+## NEW FUNCTIONALITY

+

+-   Added new plotting function `circos_genomic_density()`

+

+## FIXES

+

+-   Fixed minor issue with NA values in alluvial plots

+

+## DEPRECATIONS

+

+-   `import_parallel_Vispa2Matrices_interactive()` and

+    `import_parallel_Vispa2Matrices_auto()` are officially deprecated in

+    favor of `import_parallel_Vispa2Matrices()`

+

+## OTHER

+

+-   The package has now a more complete and functional example data set

+    for executable examples

+-   Reworked documentation

+

 # ISAnalytics 1.3.2 (2021-06-28)

 ## FIXES

new file mode 100644

@@ -0,0 +1,15 @@

+

+#' @title Deprecated functions in package \pkg{ISAnalytics}.

+#' @description These functions are provided for compatibility

+#'  with older versions of \sQuote{ISAnalytics} only,

+#'  and will be defunct at the next release.

+#' @name ISAnalytics-deprecated

+#' @details The following functions are deprecated and will be made defunct;

+#' use the replacement indicated below:

+#'

+#' * import_parallel_Vispa2Matrices_auto:

+#'  \code{\link{import_parallel_Vispa2Matrices}}

+#'  * import_parallel_Vispa2Matrices_interactive:

+#'  \code{\link{import_parallel_Vispa2Matrices}}

+#' @keywords internal

+NULL

@@ -2,7 +2,7 @@

 #' identified from genomics next generation sequencing reads for

 #' clonal tracking studies

 #'

-#' @description \lifecycle{maturing}

+#' @description \lifecycle{stable}

 #' In gene therapy, stem cells are modified using viral

 #' vectors to deliver the therapeutic transgene and replace functional

 #' properties since the genetic modification is stable and inherited in

@@ -27,8 +27,7 @@

 #'   * \code{\link{import_single_Vispa2Matrix}}

 #'   * \code{\link{import_association_file}}

 #'   * \code{\link{import_Vispa2_stats}}

-#'   * \code{\link{import_parallel_Vispa2Matrices_interactive}}

-#'   * \code{\link{import_parallel_Vispa2Matrices_auto}}

+#'   * \code{\link{import_parallel_Vispa2Matrices}}

 #' * Aggregation functions:

 #'   * \code{\link{aggregate_metadata}}

 #'   * \code{\link{aggregate_values_by_key}}

@@ -58,6 +57,7 @@

 #'   * \code{\link{sharing_heatmap}}

 #'   * \code{\link{integration_alluvial_plot}}

 #'   * \code{\link{top_abund_tableGrob}}

+#'   * \code{\link{circos_genomic_density}}

 #' * Utility functions:

 #'   * \code{\link{generate_blank_association_file}}

 #'   * \code{\link{generate_Vispa2_launch_AF}}

@@ -65,16 +65,17 @@

 #'   * \code{\link{as_sparse_matrix}}

 #'

 #' @section Vignettes:

-#' * \code{vignette("How to use import functions", package = "ISAnalytics")}

-#' * \code{vignette("Collision removal functionality",

+#' * \code{vignette("how_to_import_functions", package = "ISAnalytics")}

+#' * \code{vignette("collision_removal",

 #' package = "ISAnalytics")}

-#' * \code{vignette("Working with aggregate functions",

+#' * \code{vignette("aggregate_function_usage",

 #' package = "ISAnalytics")}

-#' * \code{vignette("Using ISAnalytics without RStudio support",

+#' * \code{vignette("report_system",

 #' package = "ISAnalytics")}

 #'

 #' @docType package

 #' @name ISAnalytics

+#' @keywords internal

 NULL

 ## usethis namespace: start

@@ -1,17 +1,17 @@

 #------------------------------------------------------------------------------#

 # Aggregate functions

 #------------------------------------------------------------------------------#

-

 #' Performs aggregation on metadata contained in the association file.

 #'

-#' \lifecycle{maturing}

+#' \lifecycle{stable}

 #' Groups metadata by the specified grouping keys and returns a

 #' summary of info for each group. For more details on how to use this function:

-#' \code{vignette("Working with aggregate functions", package = "ISAnalytics")}

+#' \code{vignette("aggregate_function_usage", package = "ISAnalytics")}

 #'

 #' @param association_file The imported association file

-#' (via link{import_association_file})

-#' @param grouping_keys A character vector of column names to form a group

+#' (via \link{import_association_file})

+#' @param grouping_keys A character vector of column names to form a grouping

+#' operation

 #' @param aggregating_functions A data frame containing specifications

 #' of the functions to be applied to columns in the association file during

 #' aggregation. It defaults to \link{default_meta_agg}. The structure of

@@ -29,17 +29,11 @@

 #' @export

 #'

 #' @examples

-#' op <- options("ISAnalytics.widgets" = FALSE, "ISAnalytics.verbose" = FALSE)

-#' path_AF <- system.file("extdata", "ex_association_file.tsv",

-#'     package = "ISAnalytics"

-#' )

-#' root_correct <- system.file("extdata", "fs.zip", package = "ISAnalytics")

-#' root_correct <- unzip_file_system(root_correct, "fs")

-#' association_file <- import_association_file(path_AF, root_correct,

-#'     dates_format = "dmy"

+#' data("association_file", package = "ISAnalytics")

+#' aggreg_meta <- aggregate_metadata(

+#'     association_file = association_file

 #' )

-#' aggregated_meta <- aggregate_metadata(association_file)

-#' options(op)

+#' head(aggreg_meta)

 aggregate_metadata <- function(association_file,

     grouping_keys = c(

         "SubjectID",

@@ -78,11 +72,12 @@ aggregate_metadata <- function(association_file,

         function_tbl = aggregating_functions

     )

     if (is.null(aggregated)) {

-        rlang::inform(paste(

+        msg <- paste(

             "No columns in `aggregating_functions$Column`",

             "was found in column names of the association",

             "file. Nothing to return."

-        ))

+        )

+        rlang::inform(msg)

     }

     aggregated

 }

@@ -145,11 +140,11 @@ default_meta_agg <- function() {

 #' Aggregates matrices values based on specified key.

 #'

-#' \lifecycle{maturing}

+#' \lifecycle{stable}

 #' Performs aggregation on values contained in the integration matrices based

 #' on the key and the specified lambda. For more details on how to use this

 #' function:

-#' \code{vignette("Working with aggregate functions", package = "ISAnalytics")}

+#' \code{vignette("aggregate_function_usage", package = "ISAnalytics")}

 #'

 #' @details

 #' ## Setting the lambda parameter

@@ -190,8 +185,8 @@ default_meta_agg <- function() {

 #' * Function should return a single value or a list/data frame:

 #' if a list or a data frame is returned as a result, all the columns

 #' will be added to the final data frame.

-#' @param x A single integration matrix (tibble) or a list of imported

-#' integration matrices (tibble)

+#' @param x A single integration matrix or a list of imported

+#' integration matrices

 #' @param association_file The imported association file

 #' @param value_cols A character vector containing the names of the

 #' columns to apply the given lambdas. Must be numeric or integer

@@ -215,26 +210,14 @@ default_meta_agg <- function() {

 #' @export

 #'

 #' @examples

-#' op <- options("ISAnalytics.widgets" = FALSE, "ISAnalytics.verbose" = FALSE)

-#' path_AF <- system.file("extdata", "ex_association_file.tsv",

-#'     package = "ISAnalytics"

-#' )

-#' root_correct <- system.file("extdata", "fs.zip", package = "ISAnalytics")

-#' root_correct <- unzip_file_system(root_correct, "fs")

-#' association_file <- import_association_file(path_AF, root_correct,

-#'     dates_format = "dmy"

-#' )

-#' matrices <- import_parallel_Vispa2Matrices_auto(

-#'     association_file = association_file, root = NULL,

-#'     quantification_type = c("fragmentEstimate", "seqCount"),

-#'     matrix_type = "annotated", workers = 2, matching_opt = "ANY"

-#' )

-#' agg <- aggregate_values_by_key(

-#'     x = matrices,

+#' data("integration_matrices", package = "ISAnalytics")

+#' data("association_file", package = "ISAnalytics")

+#' aggreg <- aggregate_values_by_key(

+#'     x = integration_matrices,

 #'     association_file = association_file,

-#'     value_cols = c("fragmentEstimate", "seqCount")

+#'     value_cols = c("seqCount", "fragmentEstimate")

 #' )

-#' options(op)

+#' head(aggreg)

 aggregate_values_by_key <- function(x,

     association_file,

     value_cols = "Value",

@@ -255,7 +238,7 @@ aggregate_values_by_key <- function(x,

         purrr::walk(x, function(df) {

             stopifnot(is.data.frame(df))

             if (.check_mandatory_vars(df) == FALSE) {

-                rlang::abort(.non_ISM_error())

+                rlang::abort(.missing_mand_vars())

             }

             if (!all(join_af_by %in% colnames(df))) {

                 rlang::abort(c(

@@ -293,7 +276,7 @@ aggregate_values_by_key <- function(x,

         })

     } else {

         if (.check_mandatory_vars(x) == FALSE) {

-            rlang::abort(.non_ISM_error())

+            rlang::abort(.missing_mand_vars())

         }

         if (!all(join_af_by %in% colnames(x))) {

             rlang::abort(c(

@@ -4,7 +4,7 @@

 #' Computes the abundance for every integration event in the input data frame.

 #'

-#' \lifecycle{maturing}

+#' \lifecycle{stable}

 #' Abundance is obtained for every integration event by calculating the ratio

 #' between the single value and the total value for the given group.

 #'

@@ -30,8 +30,9 @@

 #' @family Analysis functions

 #'

 #' @importFrom magrittr `%>%`

-#' @import dplyr

-#' @importFrom rlang .data eval_tidy parse_expr

+#' @importFrom dplyr group_by across all_of summarise left_join mutate

+#' @importFrom dplyr cur_column distinct select contains rename_with

+#' @importFrom rlang .data eval_tidy parse_expr abort

 #' @importFrom purrr map_lgl

 #' @importFrom stringr str_replace

 #' @return Either a single data frame with computed abundance values or

@@ -39,29 +40,24 @@

 #' @export

 #'

 #' @examples

-#' path <- system.file("extdata", "ex_annotated_ISMatrix.tsv.xz",

-#'     package = "ISAnalytics"

+#' data("integration_matrices", package = "ISAnalytics")

+#' abund <- compute_abundance(

+#'     x = integration_matrices,

+#'     columns = "fragmentEstimate",

+#'     key = "CompleteAmplificationID"

 #' )

-#' matrix <- import_single_Vispa2Matrix(path)

-#'

-#' # Simple integration matrix - grouping by CompleteAmplificationID

-#' abundance1 <- compute_abundance(matrix)

-#' abundance1

-#'

-#' # Keeping totals as a separate data frame

-#' abundance2 <- compute_abundance(matrix, keep_totals = "df")

-#' abundance2

+#' head(abund)

 compute_abundance <- function(x,

-    columns = "Value",

+    columns = c("fragmentEstimate_sum"),

     percentage = TRUE,

-    key = "CompleteAmplificationID",

+    key = c("SubjectID", "CellMarker", "Tissue", "TimePoint"),

     keep_totals = FALSE) {

     ## Check parameters

     stopifnot(is.data.frame(x))

     stopifnot(is.character(columns))

     stopifnot(is.character(key))

     if (.check_mandatory_vars(x) == FALSE) {

-        stop(.non_ISM_error())

+        rlang::abort(.missing_mand_vars())

     }

     stopifnot(is.logical(percentage) & length(percentage) == 1)

     if (!all(columns %in% colnames(x)) | !all(key %in% colnames(x))) {

@@ -81,7 +77,7 @@ compute_abundance <- function(x,

         }

     })

     if (any(non_num_cols)) {

-        stop(.non_num_user_cols_error(columns[non_num_cols]))

+        rlang::abort(.non_num_user_cols_error(columns[non_num_cols]))

     }

     stopifnot(is.logical(keep_totals) || keep_totals == "df")

     ## Computation

@@ -139,8 +135,8 @@ compute_abundance <- function(x,

 #' obtain a single integration matrix from individual quantification

 #' matrices.

 #'

-#' \lifecycle{maturing}

-#' Takes a list of integration matrices referring to different qunatification

+#' \lifecycle{stable}

+#' Takes a list of integration matrices referring to different quantification

 #' types and merges them in a single data frame that has multiple

 #' value columns, each renamed according to their quantification type

 #' of reference.

@@ -171,21 +167,22 @@ compute_abundance <- function(x,

 #' @export

 #'

 #' @examples

-#' op <- options("ISAnalytics.widgets" = FALSE)

-#' path <- system.file("extdata", "ex_association_file.tsv",

+#' fs_path <- system.file("extdata", "fs.zip", package = "ISAnalytics")

+#' fs <- unzip_file_system(fs_path, "fs")

+#' af_path <- system.file("extdata", "asso.file.tsv.gz",

 #'     package = "ISAnalytics"

 #' )

-#' root_pth <- system.file("extdata", "fs.zip", package = "ISAnalytics")

-#' root <- unzip_file_system(root_pth, "fs")

-#' matrices <- import_parallel_Vispa2Matrices_auto(

-#'     association_file = path, root = root,

-#'     quantification_type = c("fragmentEstimate", "seqCount"),

-#'     matrix_type = "annotated", workers = 2, patterns = NULL,

-#'     matching_opt = "ANY",

-#'     dates_format = "dmy", multi_quant_matrix = FALSE

+#' af <- import_association_file(af_path,

+#'     root = fs,

+#'     import_iss = FALSE,

+#'     report_path = NULL

 #' )

-#' total_matrix <- comparison_matrix(matrices)

-#' options(op)

+#' matrices <- import_parallel_Vispa2Matrices(af,

+#'     c("seqCount", "fragmentEstimate"),

+#'     mode = "AUTO", report_path = NULL, multi_quant_matrix = FALSE

+#' )

+#' multi_quant <- comparison_matrix(matrices)

+#' head(multi_quant)

 comparison_matrix <- function(x,

     fragmentEstimate = "fragmentEstimate",

     seqCount = "seqCount",

@@ -226,7 +223,7 @@ comparison_matrix <- function(x,

 #' Separate a multiple-quantification matrix into single quantification

 #' matrices.

 #'

-#' \lifecycle{maturing}

+#' \lifecycle{stable}

 #' The function separates a single multi-quantification integration

 #' matrix, obtained via \link{comparison_matrix}, into single

 #' quantification matrices as a named list of tibbles.

@@ -256,24 +253,11 @@ comparison_matrix <- function(x,

 #' @export

 #'

 #' @examples

-#' op <- options("ISAnalytics.widgets" = FALSE)

-#' path <- system.file("extdata", "ex_association_file.tsv",

-#'     package = "ISAnalytics"

+#' data("integration_matrices", package = "ISAnalytics")

+#' separated <- separate_quant_matrices(

+#'     integration_matrices

 #' )

-#' root_pth <- system.file("extdata", "fs.zip", package = "ISAnalytics")

-#' root <- unzip_file_system(root_pth, "fs")

-#' association_file <- import_association_file(

-#'     path = path, root = root,

-#'     dates_format = "dmy"

-#' )

-#' matrices <- import_parallel_Vispa2Matrices_auto(

-#'     association_file = association_file,

-#'     quantification_type = c("seqCount", "fragmentEstimate"),

-#'     matrix_type = "annotated", workers = 2, patterns = NULL,

-#'     matching_opt = "ANY"

-#' )

-#' separated_matrix <- separate_quant_matrices(matrices)

-#' options(op)

+#' separated

 separate_quant_matrices <- function(x,

     fragmentEstimate = "fragmentEstimate",

     seqCount = "seqCount",

@@ -315,7 +299,9 @@ separate_quant_matrices <- function(x,

         rlang::inform(.non_quant_cols_msg(to_copy))

     }

     separated <- purrr::map(num_cols, function(quant) {

-        x[c(key, to_copy, quant)] %>% dplyr::rename(Value = quant)

+        x %>%

+            dplyr::select(dplyr::all_of(c(key, to_copy, quant))) %>%

+            dplyr::rename(Value = quant)

     }) %>% purrr::set_names(names(num_cols))

     separated

 }

@@ -388,12 +374,12 @@ separate_quant_matrices <- function(x,

 #' print(example_list)

 #'

 #' filtered <- threshold_filter(example_list,

-#'                              threshold = list(first = c(20, 60),

-#'                                               third = c(25)),

-#'                              cols_to_compare = list(first = c("a", "b"),

-#'                                                     third = c("a")),

-#'                              comparators = list(first = c(">", "<"),

-#'                                                 third = c(">=")))

+#' threshold = list(first = c(20, 60),

+#' third = c(25)),

+#' cols_to_compare = list(first = c("a", "b"),

+#' third = c("a")),

+#' comparators = list(first = c(">", "<"),

+#' third = c(">=")))

 #' print(filtered)

 #'

 #' ```

@@ -411,11 +397,11 @@ separate_quant_matrices <- function(x,

 #'

 #' ```r

 #' filtered <- threshold_filter(example_list,

-#'                              threshold = list(first = c(20, 60),

-#'                                               third = c(25, 65)),

-#'                              cols_to_compare = c("a", "b"),

-#'                              comparators = list(first = c(">", "<"),

-#'                                                 third = c(">=", "<=")))

+#' threshold = list(first = c(20, 60),

+#' third = c(25, 65)),

+#' cols_to_compare = c("a", "b"),

+#' comparators = list(first = c(">", "<"),

+#' third = c(">=", "<=")))

 #' ```

 #' In this example, different threshold and comparators will be applied

 #' to the same columns in all data frames.

@@ -468,6 +454,7 @@ separate_quant_matrices <- function(x,

 #'         third = c(">=")

 #'     )

 #' )

+#' filtered

 threshold_filter <- function(x,

     threshold,

     cols_to_compare = "Value",

@@ -510,7 +497,6 @@ threshold_filter <- function(x,

 #'

 #' @family Analysis functions

 #'

-#' @import dplyr

 #' @importFrom magrittr `%>%`

 #' @importFrom rlang abort

 #'

@@ -539,16 +525,18 @@ threshold_filter <- function(x,

 #'     keep = "Value2",

 #'     key = "CompleteAmplificationID"

 #' )

-top_integrations <- function(x, n = 50,

+top_integrations <- function(x,

+    n = 20,

     columns = "fragmentEstimate_sum_RelAbundance",

-    keep = "everything", key = NULL) {

+    keep = "everything",

+    key = NULL) {

     stopifnot(is.data.frame(x))

     stopifnot(is.numeric(n) & length(n) == 1 & n > 0)

     stopifnot(is.character(keep))

     stopifnot(is.character(columns))

     stopifnot(is.null(key) || is.character(key))

     if (!.check_mandatory_vars(x)) {

-        rlang::abort(.non_ISM_error())

+        rlang::abort(.missing_mand_vars())

     }

     if (!all(columns %in% colnames(x))) {

         rlang::abort(.missing_user_cols_error(

@@ -616,28 +604,18 @@ top_integrations <- function(x, n = 50,

 #' For example:

 #'

 #' ```r

-#' ### Importing association file and matrices

-#' path_AF <- system.file("extdata", "ex_association_file.tsv",

-#' package = "ISAnalytics")

-#' root_correct <- system.file("extdata", "fs.zip",

-#' package = "ISAnalytics")

-#' root_correct <- unzip_file_system(root_correct, "fs")

-#'

-#' association_file <- import_association_file(path_AF, root_correct)

-#' matrices <- import_parallel_Vispa2Matrices_auto(

-#' association_file = association_file , root = NULL,

-#' quantification_type = c("seqCount","fragmentEstimate"),