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109 lines
4.2 KiB
109 lines
4.2 KiB
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/plot-spc-extended.R
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\name{plot_spc_ext}
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\alias{plot_spc_ext}
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\title{ggplot2 wrapper for extended spectra plotting}
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\usage{
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plot_spc_ext(
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spc_tbl,
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spc_tbl_l = NULL,
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lcols_spc = "spc",
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lcol_measure = NULL,
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lcol_measure_col_palette = "Spectral",
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lcol_measure_col_direction = -1,
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spc_id = "unique_id",
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group_id = "sample_id",
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group_id_order = TRUE,
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group_color = TRUE,
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group_color_palette = NULL,
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group_panel = TRUE,
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group_legend = FALSE,
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ncol = NULL,
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relabel_spc = TRUE,
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ylab = "Spectrum value",
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alpha = 0.5,
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line_width = 0.2,
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...
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)
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}
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\arguments{
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\item{spc_tbl}{Tibble data frame containing spectra, x-axis values, metadata
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and eventual measured variables as list-columns.}
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\item{spc_tbl_l}{List of spectral tibbles (data frames). Default is
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\code{NULL} (argument is not used).}
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\item{lcols_spc}{Character vector of spectral list-columns to be extracted.
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Default is \code{"spc"} (raw spectra).}
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\item{lcol_measure}{Character vector of length 1 denoting the column name
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of the measure columns. This argument is optional. Default is \code{NULL},
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which does not extract an additional measure column.}
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\item{lcol_measure_col_palette}{Palette value supplied to
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\code{ggplot::scale_colour_brewer()}. Default is \code{"Spectral"}, but you can set
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it to the default argument \code{1} (will use
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\code{scale_colour_brewer(..., palette = 1)}).}
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\item{lcol_measure_col_direction}{Sets the the order of colours in the scale
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that is based on a measure column. Default is \code{-1} which reverses the
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scale. Argument is passed on to the function \code{ggplot2::sclae_colour_brewer()}
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as argument \code{direction}.}
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\item{spc_id}{Character vector denoting column name for a unique spectrum ID.
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Default is \code{"unique_id"}.}
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\item{group_id}{Character vector denoting column name for the spectrum group
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ID. Default is \code{"sample_id"}. The group ID is used for
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plotting spectra by group (e.g. by using different colors or panels).}
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\item{group_id_order}{Logical that specifies whether the panel names
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derived from a numeric \code{group_id} column are reordered using ascending
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numbers. Default is \code{TRUE}.}
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\item{group_color}{Logical defining whether spectra are colored by the column
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specified by \code{group_id}.}
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\item{group_color_palette}{Character (1L) defining the diverging colour
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scales from colorbrewer.org; see \code{?scale_colour_brewer} for supported
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diverging colur types (\code{palette} argument).}
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\item{group_panel}{Logical defining whether spectra are arranged into panels
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by groups specified in \code{group_id}. Default is \code{TRUE}.}
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\item{group_legend}{Logical defining whether a legend for the \code{group_id}
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is plotted. Default is \code{FALSE}.}
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\item{ncol}{Integer vector of length 1. Defines number of columns when
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plotting panels (facets). Default is \code{NULL} (argument not used).}
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\item{relabel_spc}{Logical defining whether panels are relabeled with custom
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names for spectra types. Default is TRUE. When \code{TRUE}, arguments
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from \code{relabel_spc_types} can be passed to \code{plot_spc_ext}
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(supported via the \code{...} (ellipsis) argument)}
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\item{ylab}{Character vector or vector of type \code{"expression"} created by
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mathematical expression created by \code{expression}. Custom annotation for
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y-axis of spectra}
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\item{alpha}{Integer of length 1, from 0 to 1. Defines transparency of
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spectral lines. Default is \code{0.5} (0 is completely transparent and
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1 is no transparency).}
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\item{line_width}{Numeric vector of length 1 specifying the width of the
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spectral lines. Default is \code{0.2}.}
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\item{...}{Further arguments to be passed to \code{plot_spc_ext}. Currently,
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arguments of \code{relabel_spc_types} are supported.}
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}
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\value{
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Object of class \code{"ggplot"} (ggplot2 graph).
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}
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\description{
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\code{plot_spc_ext} is a custom plotting function developed
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within the simplerspec framework. Returns plots based on ggplot2
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(class "ggplot"). Different spectra types such as raw or preprocessed spectra
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and groups can be differentiated by different colors or by using panels
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(so called facets). Additionally, spectra can be colored based on an
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additional measure variable, e.g. determined by chemical reference analysis.
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}
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