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Plot spectral data, highlighting outliers as identified using Mahalanobis distance

Source: R/plot_spectra.R
plot_spectra.Rd

Generates a ggplot object of given spectra, with wavelength on the x axis and given spectral values on the y. Mahalanobis distance is used to calculate outliers, which are both identified on the plot. Rows from the original dataframe are printed to the console for each outlier that is identified.

Usage

plot_spectra(
  df,
  num.col.before.spectra = 1,
  window.size = 10,
  detect.outliers = TRUE,
  color = NULL,
  alternate.title = "",
  verbose = TRUE,
  wavelengths = lifecycle::deprecated()
)

Arguments

df

data.frame object containing columns of spectra. Spectral columns must be labeled with an "X" and then the wavelength (example: "X740" = 740nm). Left-most column must be unique ID. May also contain columns of metadata between the unique ID and spectral columns. Cannot contain any missing values. Metadata column names may not start with "X".

num.col.before.spectra

Number of columns to the left of the spectral matrix (including unique ID). Default is 1.

window.size

number defining the size of window to use when calculating the covariance of the spectra (required to calculate Mahalanobis distance). Default is 10.

detect.outliers

Boolean indicating whether spectra should be filtered before plotting. If TRUE, outliers are indicated by color in the resulting plot. If verbose is also set to TRUE, outlier metadata will be printed to the console. Default is TRUE.

color

String or vector of strings indicating colors to be passed to ggplot. Default is default ggplot colors.

alternate.title

String to be used as plot title. If detect.outliers is TRUE, a descriptive title will be supplied. If detect.outliers is FALSE, default is no title will be used.

verbose

If TRUE, the number of rows removed through filtering will be printed to the console. Default is TRUE.

wavelengths

DEPRECATED wavelengths is no longer supported; this information is now inferred from df column names

Value

If verbose, prints unique ID and metadata for rows identified as outliers. Returns plot of spectral data with non-outliers in blue and outliers in red. X-axis is wavelengths and y-axis is spectral values.

Author

Jenna Hershberger jmh579@cornell.edu

Examples

# \donttest{
library(magrittr)
ikeogu.2017 %>%
  dplyr::rename(unique.id = sample.id) %>%
  dplyr::select(unique.id, dplyr::everything(), -TCC) %>%
  na.omit() %>%
  plot_spectra(
    df = .,
    num.col.before.spectra = 5,
    window.size = 15,
    detect.outliers = TRUE,
    color = NULL,
    alternate.title = NULL,
    verbose = TRUE
  )
#> No outliers detected.

# }