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Add similar motif scanning and file downloads to denovo motif enrichm…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| #' Create a download button | ||
| #' | ||
| #' Creates a download button for a file or directory, suitable to embed into | ||
| #' an HTML report. | ||
| #' | ||
| #' @param path A character string specifying the path to the file or directory. | ||
| #' @param type A character string specifying the type of download. Either | ||
| #' \code{"file"} or \code{"dir"}. | ||
| #' @param add_button A logical indicating whether to add the download button to | ||
| #' the HTML report. (default = TRUE) | ||
| #' @inheritParams downloadthis::download_file | ||
| #' @inheritDotParams downloadthis::download_file | ||
| #' | ||
| #' @importFrom htmltools tagList | ||
| #' | ||
| #' @inherit downloadthis::download_file return | ||
| #' | ||
| #' @seealso \code{\link[downloadthis]{download_file}} | ||
| #' | ||
| #' @keywords internal | ||
| download_button <- function(path, | ||
| type, | ||
| button_label, | ||
| output_name = NULL, | ||
| button_type = "success", | ||
| has_icon = TRUE, | ||
| icon = "fa fa-save", | ||
| add_button = TRUE, | ||
| ...) { | ||
| if (add_button) { | ||
| wrn_msg <- paste("Package", shQuote("downloadthis"), "is required to", | ||
| "add download buttons to the HTML report. Skipping", | ||
| "download buttons...") | ||
| check_dep("downloadthis", fatal = FALSE, custom_msg = wrn_msg) | ||
|
|
||
| type <- tolower(type) | ||
| if (type == "dir") { | ||
| btn <- downloadthis::download_dir( | ||
| path = path, | ||
| output_name = output_name, | ||
| button_label = button_label, | ||
| button_type = button_type, | ||
| has_icon = has_icon, | ||
| icon = icon, | ||
| self_contained = TRUE | ||
| ) | ||
| } else if (type == "file") { | ||
| btn <- downloadthis::download_file( | ||
| path = path, | ||
| output_name = output_name, | ||
| button_label = button_label, | ||
| button_type = button_type, | ||
| has_icon = has_icon, | ||
| icon = icon, | ||
| self_contained = TRUE | ||
| ) | ||
| } | ||
|
|
||
| return(btn) | ||
| } else { | ||
| return(invisible()) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| #' Get download buttons for peak file, STREME and TOMOTM output | ||
| #' | ||
| #' @param comparison_i Index of the comparison pair group. | ||
| #' @param start_i Index of the first comparison pair. | ||
| #' @param segregated_peaks A list of peak files generated from | ||
| #' \code{\link{segregate_seqs}}. | ||
| #' @param out_dir A character vector of the directory with STREME and TOMTOM | ||
| #' output. | ||
| #' @param add_buttons A logical indicating whether to prepare download buttons. | ||
| #' @param verbose A logical indicating whether to print messages. | ||
| #' | ||
| #' @returns A list of download buttons for peak file, STREME and TOMTOM output. | ||
| #' | ||
| #' @keywords internal | ||
| get_download_buttons <- function(comparison_i, | ||
| start_i, | ||
| segregated_peaks, | ||
| out_dir, | ||
| add_buttons = TRUE, | ||
| verbose = FALSE) { | ||
| if (!add_buttons) return(NULL) | ||
| messager("Generating download buttons...", v = verbose) | ||
|
|
||
| ### Peak file button ### | ||
| btns1 <- lapply(seq_len(4), function(x) { | ||
| peak_file <- save_peak_file(segregated_peaks[[comparison_i]][[x]]) | ||
| download_button( | ||
| peak_file, | ||
| type = "file", | ||
| button_label = "Download: <code>Peak file</code>", | ||
| output_name = paste0("peak_", random_string(6)) | ||
| ) | ||
| }) | ||
|
|
||
| ### STREME output button ### | ||
| btns2 <- lapply(seq_len(4), function(x) { | ||
| streme_path <- file.path(out_dir, "streme", start_i + x - 1) | ||
| if (!dir.exists(streme_path)) return(NULL) | ||
| download_button( | ||
| streme_path, | ||
| type = "dir", | ||
| button_label = "Download: <code>STREME output</code>", | ||
| output_name = paste0("streme_", random_string(6)) | ||
| ) | ||
| }) | ||
|
|
||
| ### TOMTOM output button ### | ||
| btns3 <- lapply(seq_len(4), function(x) { | ||
| tomtom_path <- file.path(out_dir, "tomtom", start_i + x - 1) | ||
| if (!dir.exists(tomtom_path)) return(NULL) | ||
| download_button( | ||
| tomtom_path, | ||
| type = "dir", | ||
| button_label = "Download: <code>TOMTOM output</code>", | ||
| output_name = paste0("tomtom_", random_string(6)) | ||
| ) | ||
| }) | ||
|
|
||
| all_btns <- list( | ||
| peak_file = btns1, | ||
| streme_output = btns2, | ||
| tomtom_output = btns3 | ||
| ) | ||
| return(all_btns) | ||
| } |
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