plot_quantlim: Plot results of nonlinear_quantlim() and linear_quantlim()

In Vitek-Lab/MSstatsLODQ: Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Description

This function allows to plot the curve fit that is used to calculate the LOB and LOD with functions nonlinear_quantlim() and linear_quantlim(). The function outputs for each calibration curve, two pdf files each containg one plot. On the first, designated by _overall.pdf, the entire concentration range is plotted. On the second plot, designated by _zoom.pdf, the concentration range between 0 and xlim_plot (if specified in the argument of the function) is plotted. When no xlim_plot value is specified, the region close to LOB and LOD is automatically plotted.

Usage

plot_quantlim(
  spikeindata,
  quantlim_out,
  alpha,
  xlim_plot,
  width = 12,
  height = 4,
  address = ""
)

Arguments

spikeindata	Data frame that contains the experimental spiked in data. This data frame should be identical to that used as input by function functions nonlinear_quantlim() or linear_quantlim(). The data frame has to contain the following columns : CONCENTRATION, INTENSITY (both of which are measurements from the spiked in experiment) and NAME which designates the name of the assay (e.g. the name of the peptide or protein)
quantlim_out	Data frame that was output by functions nonlinear_quantlim() or linear_quantlim(). It has to contain at least the following columns: i) CONCENTRATION: Concentration values at which the value of the fit is calculated ii) MEAN: The value of the curve fit iii) LOW: The value of the lower bound of the 95\ the upper bound of the 95\ (one column with identical values) vi) LOD: The value of the LOD (one column with identical values) vii) NAME: The name of the assay (identical to that provided in the input) viii) METHOD which is LINEAR or NONLINEAR
alpha	Probability level to estimate the LOB/LOD
xlim_plot	Optional argument containing the maximum xaxis value of the zoom plot. When no value is specified, a suitable value close to LOD is automatically chosen.
width	width of the saved file. Default is 10.
height	height of the saved file. Default is 10.
address	the name of folder that will store the results. Default folder is the current working directory. The other assigned folder has to be existed under the current working directory. An output pdf file is automatically created with the default name of "QuantLim.pdf" and "QuantLim_Zoom.pdf". The command address can help to specify where to store the file as well as how to modify the beginning of the file name. If address=FALSE, plot will be not saved as pdf file but showed in window

Value

list of two ggplot2 object

Examples

## Run LOBD analysis and plot
quant_out = nonlinear_quantlim(spikeindata, Nbootstrap = 10)
plot_quantlim(spikeindata = spikeindata, quantlim_out = quant_out, 
               address = FALSE)
               

Vitek-Lab/MSstatsLODQ documentation built on Dec. 18, 2021, 6:20 p.m.