PlotRspBar: Generate bar plot to summarize response outcome by subgroups

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

Description

This function generates bar plots to compare response outcome summarization (e.g. response rate) across different groups (e.g. treatment arm, biomarker variable, demographics variable, full population vs bep, etc.)

Usage

PlotRspBar(data, outcome.var, binary = FALSE, rsp.response = c("CR", "PR"),
  rsp.nonresponse = c("SD", "PD", "NON CR/PD", "NE"), rsp.levels = c("CR",
  "PR", "SD", "NON CR/PD", "PD", "NE"), rsp.name = "Rsp", col = NULL,
  plot.count = FALSE, digits = 1, trt = NULL, trt.name = NULL,
  show.combine.trt = TRUE, compare.bep.itt = FALSE, bep = NULL,
  bep.name = NULL, itt.name = "Full", bep.indicator = 1,
  compare.var = FALSE, var = NULL, var.name = NULL,
  show.combine.var = TRUE, horiz = FALSE,
  main = "Association of response rate", sub = NULL, cex = 1,
  pdf.name = NULL, pdf.param = NULL, par.param = NULL)

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.
outcome.var	column name of the response variable (e.g. best overall response). entries with missing rsp value will be ignored in analysis.
binary	whether summarize the response rate by responder/nonresponder (if binary=TRUE), or by its original category (e.g. PD/SD/PR/CR). If binary is TRUE, responder categories and nonresponder categories should be specified in rsp.response and rsp.nonresponse (all values in the outcome column should be included in rsp.response and rsp.nonresponse), at the same time rsp.levels will be ignored. If binary is FALSE, rsp.levels should be specified to provide order of the categories. At the same time rsp.response and rsp.nonresponse will be ignored.
rsp.response	categories that should be considered as responder.
rsp.nonresponse	categories that should be considered as non responder.
rsp.levels	vector that indicates how to sort the response categories. This parameter will be ignored if binary is TRUE.
rsp.name	Display name for the responders. Default is "rsp".
col	color for different categories
plot.count	default is FALSE. By default percentages will be shown. If it is TRUE, will show counts instead
digits	see pdf. Number of digits to display for the response rate.
trt	column name that indicates treatment variable. If this is not NULL, the program will summarize the response outcome within each treatment arm.
trt.name	treatment name to display
show.combine.trt	if this is TRUE, will show summarization of combined data across treatment arms as well
compare.bep.itt	whether want to generate two groups of bars to compare the summary statistics in full population (e.g. ITT) vs in BEP. If this is TRUE, paramemeter bep should be specified. If this is FALSE, parameters bep, bep.name, itt.name, bep.indicator will be ignored
bep	name of the column which indicates biomarker evaluable population. If it is null, patients who have non NA records in biomarker variable will be used as BEP.
bep.name	preferred display name of the biomarker evaluable population. If it is NULL, bep will be used.
itt.name	preferred display name of the full population (e.g. ITT). If it is NULL, "All" will be used.
bep.indicator	In the subpopulation column, which value is used to define the biomarker evaluable population.
compare.var	whether want to generate multiple groups of bars to compare the summary statistics in subgroups defined by var (e.g. categorical demographics or biomarker variable) . If this is TRUE, paramemeter var should be specified. If this is FALSE, parameters var, var.name, show.combine.var will be ignored
var	a vector of covariate names - the clinical covariate to test
var.name	preferred display names of the clinical covariates If it is NULL, var will be used.
show.combine.var	if this is TRUE, will show summarization of combined data across var levels as well
horiz	whether show barplot horizontally
main	main title of the barplot. Default is "Association of biomarker expression with response rate".
sub	footnote under the bar plot. Default is NULL.
cex	cex
pdf.name	name of output pdf file. If it's NULL, the plots will be displayed but not saved as pdf. Default is "rsp.barplot.pdf".
pdf.param	list of parameters that define pdf graphics device. See pdf. Default is list(width=6, height=4.5).
par.param	list of parameters that define graphcial parameters. See par. Default is list(mar=c(4,4,3,2)).

Value

a bar plot that summarizes response outcome

Author(s)

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

Examples

data(input)
PlotRspBar (input, outcome.var="Response",
           binary=TRUE,
           rsp.response=c("CR","PR"),
           rsp.nonresponse=c("SD", "PD","NON CR/PD","NE",NA),
           trt="Arm",
           compare.var=TRUE,
           var="KRAS.mutant")

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