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Autofluorescence QC Plot

Source: R/af_qc_plot.R
af.qc.plot.Rd

This function plots a comparison between the user's fluorophore spectrum, from spectra, and an identified autofluorescence spectrum that may represent contamination. Quality control is performed using cosine similarity between the two spectral profiles.

Usage

af.qc.plot(
  af.spectra,
  spectra,
  qc.table,
  af.color = "black",
  fluor.color = "blue",
  af.line.type = "solid",
  fluor.line.type = "dotted",
  linewidth = 1,
  plot.dir = "./figure_autofluorescence",
  filename = "autofluorescence_qc_report.pdf"
)

Arguments

af.spectra

Matrix or dataframe containing autofluorescence spectral signatures. This should be in format AFn x detectors. Row names will be used as the names.

spectra

Matrix or dataframe containing spectral data. This should be in format fluorophores x detectors. Row names will be used as the fluorophore names. Column names will be used as the detectors (channels).

qc.table

Dataframe containing the pre-screened problematic AF spectra and the fluorophores to which they are similar. Format: columes named AF, Fluorophore and Similarity containing, respectively, the names of the AF spectra, the names of the similar fluorophores and the cosine similarity values.

af.color

Color for the line representing the user's autofluorescence spectrum from the unstained reference control. Default is black.

fluor.color

Color for the line representing the similar fluorophore spectrum. Default is blue.

af.line.type

Line style for the line representing the user's AF spectrum. Default is solid.

fluor.line.type

Line style for the line representing thefluorophore spectrum. Default is dotted.

linewidth

Width of the line for the spectral traces. Default is 1.

plot.dir

Directory where the files will be saved. Default is ./figure_autofluorescence.

filename

Name for the output PDF file. Default is autofluorescence_qc_report.pdf.

Value

None. Plots are saved to a PDF in plot.dir.

See also