-
Notifications
You must be signed in to change notification settings - Fork 46
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #361 from lgatto/SpectrumList
Add new class SpectrumList
- Loading branch information
Showing
9 changed files
with
1,125 additions
and
10 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| #' @rdname Spectra | ||
| #' | ||
| #' @section Constructor: | ||
| #' | ||
| #' New [Spectra] can be created with the `Spectra(...)` function | ||
| #' where `...` can either be a single [Spectrum-class] object or a `list` of | ||
| #' `Spectrum` objects ([Spectrum1-class] and/or [Spectrum2-class]). | ||
| #' | ||
| #' @param ... For `Spectra`: [Spectrum-class] object(s) or a `list` of | ||
| #' [Spectrum-class] objects. | ||
| #' | ||
| #' @param elementMetadata For `Spectra`: [DataFrame] with optional information | ||
| #' that should be added as metadata information (`mcols`) to the object. | ||
| #' The number of rows has to match the number of [Spectrum-class] objects, | ||
| #' each row is expected to represent additional metadata information for | ||
| #' one spectrum. | ||
| #' | ||
| #' @author Johannes Rainer | ||
| #' | ||
| #' @md | ||
| #' | ||
| #' @examples | ||
| #' | ||
| #' ## Create from Spectrum objects | ||
| #' sp1 <- new("Spectrum1", mz = c(1, 2, 4), intensity = c(4, 5, 2)) | ||
| #' sp2 <- new("Spectrum2", mz = c(1, 2, 3, 4), intensity = c(5, 3, 2, 5), | ||
| #' precursorMz = 2) | ||
| #' | ||
| #' spl <- Spectra(sp1, sp2) | ||
| #' spl | ||
| #' spl[[1]] | ||
| #' | ||
| #' ## Add also metadata columns | ||
| #' mcols(spl)$id <- c("a", "b") | ||
| #' mcols(spl) | ||
| #' | ||
| #' ## Create a Spectra with metadata | ||
| #' spl <- Spectra(sp1, sp2, elementMetadata = DataFrame(id = c("a", "b"))) | ||
| #' | ||
| #' mcols(spl) | ||
| #' mcols(spl)$id | ||
| Spectra <- function(..., elementMetadata = NULL) { | ||
| args <- list(...) | ||
| if (length(args) == 1L && is.list(args[[1L]])) | ||
| args <- args[[1L]] | ||
| new("Spectra", listData = args, elementMetadata = elementMetadata) | ||
| } | ||
|
|
||
| .show_Spectra <- function(x, margin = "", print.classinfo = FALSE) { | ||
| cat("Spectra with", length(x), "spectra and", length(mcols(x)), | ||
| "metadata column(s):\n") | ||
| if (length(x)) { | ||
| out <- S4Vectors:::makePrettyMatrixForCompactPrinting( | ||
| x, .make_naked_matrix_from_Spectra) | ||
| if (print.classinfo) { | ||
| .COL2CLASS <- c(msLevel = "integer", rtime = "numeric", | ||
| peaksCount = "integer") | ||
| classinfo <- S4Vectors:::makeClassinfoRowForCompactPrinting( | ||
| x, .COL2CLASS) | ||
| out <- rbind(classinfo, out) | ||
| } | ||
| if (nrow(out)) | ||
| rownames(out) <- paste0(margin, rownames(out)) | ||
| print(out, quote = FALSE, right = TRUE, max = length(out)) | ||
| } | ||
| } | ||
|
|
||
| .short_spectrum_info <- function(x) { | ||
| c(msLevel = x@msLevel, rtime = ifelse(length(x@rt), x@rt, NA_real_), | ||
| peaksCount = peaksCount(x)) | ||
| } | ||
|
|
||
| .make_naked_matrix_from_Spectra <- function(x) { | ||
| x_len <- length(x) | ||
| mcls <- mcols(x, use.names = FALSE) | ||
| x_mcls_len <- if (is.null(mcls)) 0L else ncol(mcls) | ||
| res <- do.call(rbind, lapply(x, .short_spectrum_info)) | ||
| res <- apply(res, 2, format, digits = 6) | ||
| if (!is.matrix(res)) | ||
| res <- t(as.matrix(res)) | ||
| res <- res[, c("msLevel", "rtime", "peaksCount"), drop = FALSE] | ||
| if (x_mcls_len > 0) { | ||
| tmp <- do.call(data.frame, c(lapply(mcls, showAsCell), | ||
| list(check.names = FALSE))) | ||
| res <- cbind(res, `|` = rep.int("|", x_len), as.matrix(tmp)) | ||
| } | ||
| res | ||
| } |
Oops, something went wrong.