R/internal-msgs.R

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

### Convenience functions for errors and warnings ###

.af_correctness_warning <- function() {
    paste(
        "Columns found in the imported association file differ from",
        "the default values in 'association_file_columns()' ",
        "problems may arise in some functions"
    )
}

# Signals the user that file system alignment can't be performed because
# 'PathToFolderProjectID' is missing.
# USED IN:
# - .check_file_system_alignment
.af_missing_pathfolder_error <- function() {
    c("Column 'PathToFolderProjectID' is missing",
        x = "Can't proceed with file system alignment",
        i = paste(
            "To import metadata without performing file system aligment",
            "set the parameter 'root' to NULL"
        )
    )
}

# Signals the user that the column
# 'Path' is missing (needed for matrix import).
# USED IN:
# - import_parallel_Vispa2Matrices
.af_missing_path_error <- function() {
    c("Column 'Path' not found in the association file",
        x = paste(
            "File system alignment is necessary for this step. Please",
            "re-import the association file with the alignment feature"
        )
    )
}

# Produces a mini-report to print after file reading only if verbose is active
# USED IN:
# - import_associaton_file
.summary_af_import_msg <- function(pars_prob, dates_prob, cols_prob, crit_na,
    checks) {
    c(
        "*** Association file import summary ***",
        i = "For detailed report please set option 'ISAnalytics.widgets' to TRUE",
        paste0("Parsing problems detected: ", !is.null(pars_prob)),
        paste0("Date parsing problems: ", !is.null(dates_prob)),
        paste0("Column problems detected: ", !is.null(cols_prob)),
        paste0("NAs found in important columns: ", !is.null(crit_na)),
        paste0("File system alignment: ", checks)
    )
}

# Warns the user that the input file is in excel format and it is not
# reccommended for potential parsing issues.
# USED IN:
# - .read_af
.xls_file_warning <- function() {
    c("Warning: file in xls/xlsx format",
        i = paste(
            "The use of xls/xlsx is discouraged as it can lead to",
            "potential problems in parsing data. Use of *.tsv or *.csv",
            "is recommended."
        ),
        "Carefully review the data after importing!"
    )
}

.widgets_error <- function() {
    paste("Unable to produce widget report, skipping this step")
}

.widgets_save_error <- function() {
    paste("Unable to save widget to file, skipping this step")
}

# Produces a mini-report to print after file reading only if verbose is active
# USED IN:
# - import_single_Vispa2Matrix
.summary_ism_import_msg <- function(df_type, annotated, dims, mode) {
    c(
        "*** File info *** ",
        paste("--- Matrix type:", df_type),
        paste("--- Annotated:", annotated),
        paste("--- Dimensions:", paste0(dims, collapse = " x ")),
        paste("--- Read mode: ", mode)
    )
}

# Produces a mini-report to print after file reading only if verbose is active
# USED IN:
# - import_parallel_Vispa2Matrix
#' @importFrom dplyr select
#' @importFrom tidyr unnest
.summary_ism_par_import_msg <- function(fimported, files_to_import,
    files_found) {
    if (getOption("ISAnalytics.verbose") == TRUE) {
        print("--- REPORT: FILES IMPORTED ---")
        print(fimported, width = Inf)
        print("--- SUMMARY OF FILES CHOSEN FOR IMPORT ---")
        print(files_to_import, width = Inf)
        print("--- INTEGRATION MATRICES FOUND REPORT ---")
        unnested <- tidyr::unnest(files_found %>%
            dplyr::select(
                -.data$Files_count
            ),
        cols = c(.data$Files)
        )
        print(unnested,
            n = nrow(unnested), width = Inf
        )
    }
}

# Warns the user that the file in input is compressed but the compression
# format is not supported by fread.
# USED IN:
# - import_single_Vispa2Matrix
# - .read_af
.unsupported_comp_format_inf <- function() {
    c(paste(
        "Warning: compression format not",
        "supported by fread"
    ),
    i = "File will be read using readr"
    )
}

# Error that signals the integration matrix to import is malformed, aka
# it does not contain mandatory variables or does not have a standard structure
# USED IN:
# - import_single_Vispa2Matrix
.malformed_ISmatrix_error <- function() {
    c("The input integration matrix seems to be malformed",
        x = "Non standard column structure detected",
        i = paste(
            "Matrix should contain either these columns: [",
            paste0(mandatory_IS_vars(), collapse = ", "),
            "], or",
            "'IS_genomicID'",
            "but not both or a combination of the two."
        )
    )
}

# General error, used in multiple functions: signals that the input is
# formally not considered an integration matrix
.non_ISM_error <- function() {
    paste(
        "One or more elements in x are not integration matrices.",
        "Aborting."
    )
}

# @keywords internal
.missing_value_col_error <- function() {
    paste(
        "The value column is missing or it contains non-numeric data.",
        "The column is needed for this operation.",
        "Aborting."
    )
}

# @keywords internal
.missing_complAmpID_error <- function() {
    paste(
        "The `CompleteAmplificationID` column is missing.",
        "The column is needed for this operation.",
        "Aborting."
    )
}

.warning_update_after_alignment <- function(root) {
    paste0("One or more projects were not found in the file ",
        "system starting from ", root, ", please check your ",
        "association file for errors and/or your file system.",
        "Until you re-import the association file these ",
        "missing files will be ignored.",
        collapse = ""
    )
}

# @keywords internal
.quant_types_error <- function() {
    paste(
        "The list names must be quantification types",
        ", see quantification_types() for reference"
    )
}

# @keywords internal
.missing_num_cols_error <- function() {
    paste("No numeric columns found")
}

# @keywords internal
.non_quant_cols_msg <- function(x) {
    paste(c(
        "Found numeric columns that are not quantification values:",
        "these columns will be copied in all resulting matrices.",
        "Found: ", x
    ), collapse = "\n")
}

# @keywords internal
.non_quant_cols_error <- function() {
    paste(
        "No quantification values columns found. Did you set the function",
        "parameters correctly?"
    )
}

# @keywords internal
.max_val_col_warning <- function(x) {
    paste0("Column for max value `", x, "` not found in numeric columns.")
}

# @keywords internal
.using_val_col_warning <- function(x) {
    paste(c(
        .max_val_col_warning(x),
        "Using `Value` column as reference instead."
    ), collapse = "\n")
}

# @keywords internal
.max_val_stop_error <- function(x) {
    paste(c(
        .max_val_col_warning(x),
        "Did you set `max_value_column` parameter correctly?"
    ),
    collapse = "\n"
    )
}

# @keywords internal
.nas_introduced_msg <- function() {
    paste("NAs were introduced while producing the data frame.",
        "The possible cause for this is:",
        "some quantification matrices were not imported for all pools",
        sep = "\n"
    )
}

#---- USED IN : remove_collisions ----
.no_collisions_msg <- function() {
    paste("No collisions found for the given matrix, nothing to do")
}

#---- USED IN : threshold_filter ----

# @keywords internal
.threshold_err <- function() {
    paste("The parameter `threshold` must be numeric or integer")
}

# @keywords internal
.comparators_err <- function() {
    paste(c(
        "The parameter `comparators` must be a character vector",
        "and in the allowed range: ", c("<", ">", "==", "!=", ">=", "<=")
    ),
    collapse = " "
    )
}

# @keywords internal
.names_list_param_err <- function() {
    paste(
        "If provided as lists, parameters must have",
        "names equal to names in x"
    )
}

# @keywords internal
.diff_leng_args <- function() {
    paste0("Parameters `threshold`, `cols_to_compare` and `comparators`",
        "have different lengths",
        collapse = " "
    )
}

# Error message: notifies the user that one or more column names specified
# as parameters were not found in the data frame column names
# USED IN:
# - compute_abundance
# - top_integrations
.missing_user_cols_error <- function(missing_cols) {
    c(paste(
        "Some or all of the input column names were not found",
        "in the data frame"
    ),
    i = paste(
        "Columns missing:",
        paste0(missing_cols, collapse = ", ")
    )
    )
}

# @keywords internal
.missing_user_cols_list_error <- function(set, name) {
    paste0(c(
        "Columns ",
        paste0(set, collapse = ", "),
        " not found in x$", name
    ), collapse = "")
}

# Error message: notifies the user that one or more column names specified
# as parameters are not numeric
# USED IN:
# - compute_abundance
.non_num_user_cols_error <- function(non_num) {
    paste(
        paste(
            "Some or all of the input column names are not numeric",
            "or integer in the data frame"
        ),
        "Non-numeric columns:",
        paste0(non_num, collapse = ", "),
        sep = "\t"
    )
}

# @keywords internal
.list_params_err <- function() {
    paste(
        "Provided parameters `threshold`, `comparators`",
        "or `cols_to_compare` are lists when input is a",
        "data frame. Please see ?threshold_filter for more",
        "info."
    )
}

# @keywords internal
.unnamed_list_err <- function() {
    paste(
        "Some parameters were provided as named lists",
        "but x is unnamed list. Give names to x or",
        "change the parameters, see ?threshold_filter",
        "for details"
    )
}

# @keywords internal
.param_names_not_in_list_err <- function() {
    paste(
        "Named lists in parameters must have the same",
        "names as x, see ?threshold_filter",
        "for details"
    )
}

# @keywords internal
.param_names_not_equal_err <- function() {
    paste(
        "Some list parameters between `threshold`,",
        "`cols_to_compare` or `comparators` miss elements.",
        "See ?threshold_filter for details"
    )
}

#---- USED IN : CIS_grubbs ----
.missing_annot <- function() {
    paste(
        "Annotation columns are missing but are required for",
        "the function correct execution"
    )
}

.non_standard_annotation_structure <- function() {
    paste(
        "The genomic annotation file must have the standard UCSC format,",
        "see ?CIS_grubbs for details"
    )
}

#---- USED IN : cumulative_count_union ----
.agg_with_null_meta_err <- function() {
    paste(
        "Matrix aggregation can't be performed without the ",
        "association file, please specify one in the `metadata` parameter"
    )
}

.key_without_tp_err <- function() {
    paste("The sample key must contain the time point column")
}

.key_not_found <- function() {
    paste("One or more columns in the sample keys were not found in x")
}