correlationPlotLiP: Plot run correlation for provided LiP and TrP experiment.

In devonjkohler/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Description

Plot run correlation for provided LiP and TrP experiment.

Usage

correlationPlotLiP(
  data,
  method = "pearson",
  value_columns = "INTENSITY",
  x.axis.size = 10,
  y.axis.size = 10,
  legend.size = 10,
  width = 10,
  height = 10,
  address = ""
)

Arguments

data	output of MSstatsLiP converter function. Must include at least ProteinName, Run, and Intensity columns
method	one of "pearson", "kendall", "spearman". Default is pearson.
value_columns	one of "INTENSITY" or "ABUNDANCE". INTENSITY is the raw data, whereas ABUNDANCE is the log transformed INTENSITY column. INTENSITY is default.
x.axis.size	size of axes labels, e.g. name of the comparisons in heatmap, and in comparison plot. Default is 10.
y.axis.size	size of axes labels, e.g. name of targeted proteins in heatmap. Default is 10.
legend.size	size of legend for color at the bottom of volcano plot. Default is 10.
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 "VolcanoPlot.pdf" or "Heatmap.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

plot or pdf

Examples

## Use output of dataSummarizationLiP function
correlationPlotLiP(MSstatsLiP_Summarized, address = FALSE)

devonjkohler/MSstatsLiP documentation built on Dec. 19, 2021, 11:01 p.m.