protti: plot_drc_4p – R documentation

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plot_drc_4p

Plotting of four-parameter dose response curves

Description

Function for plotting four-parameter dose response curves for each group (precursor, peptide or protein), based on output from fit_drc_4p function.

Usage

plot_drc_4p(
  data,
  grouping,
  response,
  dose,
  targets,
  unit = "uM",
  y_axis_name = "Response",
  facet = TRUE,
  scales = "free",
  x_axis_scale_log10 = TRUE,
  export = FALSE,
  export_name = "dose-response_curves"
)

Arguments

`data`	A data frame that is obtained by calling the `fit_drc_4p` function.
`grouping`	The name of the column containing precursor, peptide or protein identifiers.
`response`	The name of the column containing response values, eg. log2 transformed intensities.
`dose`	The name of the column containing dose values, eg. the treatment concentrations.
`targets`	A character vector that specifies the names of the precursors, peptides or proteins (depending on `grouping`) that should be plotted. This can also be `"all"` if plots for all curve fits should be created.
`unit`	A character vector specifying the unit of the concentration.
`y_axis_name`	A character vector specifying the name of the y-axis of the plot.
`facet`	A logical indicating if plots should be summarised into facets of 20 plots. This is recommended for many plots.
`scales`	A character vector that specifies if the scales in faceted plots (if more than one target was provided) should be `"free"` or `"fixed"`.
`x_axis_scale_log10`	A logical indicating if the x-axis scale should be log10 transformed.
`export`	A logical indicating if plots should be exported as PDF. The output directory will be the current working directory. The name of the file can be chosen using the `export_name` argument. If only one target is selected and `export = TRUE`, the plot is exported and in addition returned in R.
`export_name`	A character vector providing the name of the exported file if `export = TRUE`.

Value

If targets = "all" a list containing plots for every unique identifier in the grouping variable is created. Otherwise a plot for the specified targets is created with maximally 20 facets.

Examples

## Not run: 
plot_drc_4p(
  data,
  grouping = eg_precursor_id,
  response = intensity,
  dose = concentration,
  targets = c("ABCDEFK")
)

## End(Not run)

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release