PlotDens: Plot Density

In lengning/gClinBiomarker: gClinBiomarker: an R package for clinical biomarker analyses

Description

Generate density plot for a continuous covariate.

Usage

PlotDens(data, var, log2 = FALSE, col = "blue", text.font = 3,
  main = paste("Distribution of", var), add.num = 0, xlab = paste(var,
  ifelse(log2 == TRUE, "(log2 scale)", "")), pdf.name = NULL,
  pdf.param = list(width = 6, height = 4.5), par.param = list(mar = c(4, 4,
  3, 2)))

Arguments

data	Input data frame. Rows are patients and columns are variables (e.g. demographics variables, time to event variables, biomarker variables, treatment indicator, etc.). One patient per row.
var	Name of a variable (e.g. a biomarker variable). Should be in colnames of data.
log2	If TRUE, computes binary (i.e. base 2) logarithm. Default is FALSE.
col	The color of the line segments. Default is blue.
text.font	Legend text font size. Default is 3.
main	The main title. Default is paste("Distribution of", var). A variable name will be added at the end of the title.
add.num	The constant to add to all values. Helps to avoid applying log transformation on 0 or negative values. Default is 0.
xlab	X axis label. Default is paste(var, ifelse(log2 == TRUE, "(log2 scale)", "")). A variable name will be added at the beginning of the label.
pdf.name	Name of output pdf file. If it's NULL (default), the plots will be displayed but not saved as pdf.
pdf.param	A list of parameters that define pdf graphics device. See pdf. Default is list(width=6, height=4.5).
par.param	A list of parameters that define graphcial parameters. See par. Default is list(mar=c(4,4,3,2)).

Value

Histogram and density will be shown. Summary statistics will be also shown on the plots.

Author(s)

Alexey Pronin [e-mail], Ning Leng [e-mail], and previous team members (see DESCRIPTION)

Examples

data(input)
PlotDens(data=input, var="KRAS.exprs", log2=TRUE)

lengning/gClinBiomarker documentation built on May 9, 2019, 2:55 p.m.