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

View source: R/correlationPlotLiP.R

correlationPlotLiPR Documentation

Plot run correlation for provided LiP and TrP experiment.

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)

Vitek-Lab/MSstatsLiP documentation built on April 5, 2024, 3:25 a.m.