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v0.4.2, new plot functions, sped up alignment for ms search
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| #' Plot spectrum from peak table | ||
| #' | ||
| #' Plots the trace and/or spectrum for a given peak in peak table. | ||
| #' | ||
| #' Can be used to confirm the identity of a peak or check that a particular | ||
| #' column in the peak table represents a single compound. Can also be used | ||
| #' to create simple box-plots to examine the distribution of a peak with respect | ||
| #' to variables defined in sample metadata. | ||
| #' | ||
| #' @importFrom graphics title boxplot | ||
| #' @importFrom stats as.formula | ||
| #' @param x A \code{ms.alignment} object. | ||
| #' @param col A vector specifying the peak(s) that you wish to plot. | ||
| #' @param plot_spectrum Logical. If TRUE, plots the mass spectrum of the chosen | ||
| #' peak. Defaults to TRUE. | ||
| #' @param box_plot Logical. If TRUE, plots box plot using factors | ||
| #' defined by \code{vars}. | ||
| #' @param vars Independent variables for boxplot. Righthand side of formula. | ||
| #' @param spectrum_labels Logical. If TRUE, plots labels on maxima in spectral | ||
| #' plot. Defaults to TRUE. | ||
| #' @param engine Which plotting engine to use: either \code{base} or \code{plotly}. | ||
| #' @param ... Additional arguments to \code{\link[graphics]{boxplot}}. | ||
| #' @return No return value. | ||
| #' @section Side effects: | ||
| #' | ||
| #' If \code{plot_spectrum} is TRUE, plots the spectrum for the specified chromatogram | ||
| #' at the specified retention time. The spectrum is a single row from the chromatographic | ||
| #' matrix. | ||
| #' | ||
| #' If \code{box_plot} is TRUE, produces a \code{\link[graphics]{boxplot}} from the | ||
| #' specified peak with groups provided by \code{vars}. | ||
| #' | ||
| #' @author Ethan Bass | ||
| #' @rdname plot.peak_table | ||
| #' @concept Visualization | ||
| #' @export | ||
|
|
||
| plot.ms_alignment <- function(x, col, plot_spectrum = TRUE, | ||
| box_plot = FALSE, vars = NULL, | ||
| spectrum_labels = TRUE, | ||
| engine = c("base", "plotly"), ...){ | ||
| engine <- match.arg(engine, c("base", "plotly")) | ||
| for (col in col){ | ||
| if (plot_spectrum){ | ||
| ms_plot_spectrum(x = x, col = col, plot_labels = spectrum_labels, | ||
| type = engine) | ||
| } | ||
| if (box_plot){ | ||
| if (!is.data.frame(x$sample_meta)){ | ||
| stop("Attach metadata to `peak_table` to make a boxplot.") | ||
| } | ||
| if (is.null(vars)){ | ||
| stop("Must provide independent variable(s) (`var`) to make a boxplot.") | ||
| } | ||
| boxplot(as.formula(paste("x[['tab']][,col]", vars, sep="~")), | ||
| data = x$sample_meta, | ||
| main = paste(col, '\n', 'RT = ', | ||
| round(as.numeric(x$peak_meta[col, "Average.Rt.min."]), 2)), | ||
| ylab = "abs", xlab = "", ...) | ||
| } | ||
| } | ||
| } | ||
|
|
||
| #' Make boxplot from MS peak table. | ||
| #' | ||
| #' The function can take multiple response variables on the left hand side of the | ||
| #' formula (separated by \code{+}). In this case, a separate boxplot will be | ||
| #' produced for each response variable. | ||
| #' | ||
| #' @param x A peak_table object | ||
| #' @param formula A formula object | ||
| #' @param ... Additional arguments to \code{\link[graphics]{boxplot}} | ||
| #' @importFrom stats reformulate terms | ||
| #' @importFrom graphics boxplot | ||
| #' @concept Visualization | ||
| #' @export | ||
|
|
||
| boxplot.ms_alignment <- function(x, formula, ...){ | ||
| if (missing(formula)){ | ||
| stop("Please provide a `formula` to make a boxplot.") | ||
| } | ||
| lhs <- get_lhs_vars(formula) | ||
| for (li in lhs){ | ||
| response <- paste0("x[['tab']][,'", li, "']") | ||
| form <- reformulate(labels(terms(formula)), response = response) | ||
|
|
||
| idx <- ifelse(!is.na(x$peak_meta[col,"Average.RI"]), | ||
| paste0("RI: ", x$peak_meta[col,"Average.RI"]), | ||
| paste0("RT: ", x$peak_meta[col,"Average.Rt.min."]) | ||
| ) | ||
| title <- paste(li, idx, sep = "\n") | ||
| boxplot(form, | ||
| data = x$sample_meta, | ||
| main = title, | ||
| ylab = "", xlab = "", ...) | ||
| } | ||
| } | ||
|
|
||
| #' Extract variables from the left-hand-side of a formula. | ||
| #' @param formula A \code{\link{formula}} object. | ||
| #' @importFrom Formula Formula | ||
| #' @noRd | ||
| #' @note Adapted from https://github.com/adibender/pammtools/blob/master/R/formula-utils.R | ||
| #' (c) Copyright © 2017 Andreas Bender and Fabian Scheipl under MIT license: | ||
| #' Permission is hereby granted, free of charge, to any person obtaining a copy of | ||
| #' this software and associated documentation files (the “Software”), to deal in | ||
| #' the Software without restriction, including without limitation the rights to use, | ||
| #' copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the | ||
| #' Software, and to permit persons to whom the Software is furnished to do so, | ||
| #' subject to the following conditions: | ||
| #' | ||
| #' The above copyright notice and this permission notice shall be included in all | ||
| #' copies or substantial portions of the Software. | ||
| #' | ||
| #' THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| #' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| #' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| #' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, | ||
| #' WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN | ||
| #' CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. | ||
|
|
||
| get_lhs_vars <- function(formula) { | ||
| if (is.character(formula) ) formula <- as.formula(formula) | ||
| form <- formula(Formula::Formula(formula), lhs = TRUE, rhs = FALSE) | ||
| all.vars(form) | ||
| } |
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