uwLineGraph: Line Graph of Means or Medians

In jbirstler/biostatrpts: Functions for UW-Biostatistics Report Creation

Description

Line Graph of Means or Medians over multiple factor levels, most often time points

Usage

uwLineGraph(
  data,
  metricName,
  trxName,
  factorName,
  LatexFileName = NULL,
  plotMean = FALSE,
  pch = NULL,
  colScale = FALSE,
  yLim = NULL,
  yLab = "",
  xLab = "",
  pTitle = NULL,
  refLines = TRUE,
  Legend = TRUE,
  LegendLoc = "topright",
  LegendCex = 0.7,
  printPVals = TRUE,
  pTest = c("wilcox", "t", "kruskal", "anova"),
  pExclude = NULL,
  trxControl = NULL,
  pairDiffTab = FALSE,
  ptIDname = NULL,
  BaseLevel = NULL,
  numDec = 2,
  rowLines = list(c(FALSE), c(FALSE)),
  caption = list(c(NULL), c(NULL)),
  firstCol.name = NULL,
  Ropen = FALSE,
  ...
)

Arguments

data	Data frame containing the necessary variables described below
metricName	(string) Name of numeric column in data
trxName	(string) Name of Treatment column in data. There will be separate lines for each treatment level
factorName	(sting) Name of factor column in data. There will be plotted points of the mean and median of each treatment at each factor level. Factor levels are on the x-axis and it is recommend that it is an ordered factor
LatexFileName	(string) Giving the folder and file(ending in .tex) for the LaTeX table to be saved., length=2 if pairDiffTab=TRUE
plotMean	(logical) TRUE plots mean values, FALSE plots median values
pch	(vector) Numeric specifying which plotting points should be used to represent different treatment levels. Default is c(19,21,23,24,25,7,8,17,0,15)[1:nlevels(trxName)]
colScale	(logic or vector) Default is FALSE which plots the lines and points on a gray scale. TRUE plots the lines and points on a color scale like so: c('black','red','blue','forestgreen', 'gold2','violet','brown','chartreuse','lightgreen', 'magenta')[1:nlevels(trxName)], or you can put in your own set of colors; length should match nlevels of trxName
yLim	Limits of y axis, default makes sure there is a tick mark above the max value and below the min value
yLab	(string) y-axis Label
xLab	(string) x-axis Label
pTitle	(string) Plot Title
refLines	(logical) TRUE plots dotted lines across the plot at each y-axis tick, FALSE does not
Legend	(logical) Show Legend in plot or not
LegendLoc	(string) Placement of Legend according legend()
LegendCex	(numeric) Magnification factor of the legend size
printPVals	(logical) TRUE corresponds to p-values placed in Latex table
pTest	(string) Only if printPVals=TRUE: Which test should be conducted out of wilcoxon, t.test, anova, or kruskal. Starting letter will suffice
pExclude	(string) Only if printPVals=TURE: List the treatment levels (other than control level) that you do not want to report p-values for. Does not apply when pTest is anova or kruskal
trxControl	(string) Only if printPVals=TRUE: List which level of trxName is considered the control group
pairDiffTab	(logical) TRUE if paired differences want to be examined because factorName indicates time points of repeated measures.
ptIDname	(string) Only if pairDiffTab=TRUE: Column name in data that indicates patient ID's
BaseLevel	(sring) Only if pairDiffTab=TRUE: Level in factorName that should be considered the baseline level for differencing
numDec	(numeric) Number specifying how many decimals the summary statistics should be rounded too.
rowLines	(list of two logical vectors) Used in specifying horizontal lines in the LaTeX tables. First list spot is for regular table, second is for difference table. If pairDiffTab=FALSE, then this needs not be a list. See ?uwLatex
caption	(list of two logical vectors) Used in specifying the captions in the LaTeX tables. First list spot is for regular table, second is for difference table. If pairDiffTab=FALSE, then this needs not be a list. See ?uwLatex
firstCol.name	(string) Specifies the first column name in the LaTeX tables. Defaults to factorName
Ropen	(logical) TRUE collapses across treatment levels and plots mean or median for all patients
...	Any other arguments that can be passed to uwLatex

Examples

TRT <- rep(rep(c("A", "B", "C"), c(20, 20, 20)), 4)

ptID <- rep(1:60, 4)
ptID <- factor(ptID)

numVar <- c(
  rnorm(20, 0, 1), rnorm(20, 1, 1), rnorm(20, 2, 1), rnorm(20, 3, 1),
  rnorm(20, 3, 1), rnorm(20, 10, 1), rnorm(20, 2, 3), rnorm(20, 0, 1),
  rnorm(20, 6, 1), rnorm(20, 1, 3), rnorm(20, 2, 5), rnorm(20, 3, 1)
)

timeVar <- rep(c("Baseline", "3 Months", "6 Months", "12 Months"), c(60, 60, 60, 60))
timeVar <- ordered(
  timeVar,
  c("Baseline", "3 Months", "6 Months", "12 Months")
)

df <- data.frame(TRT, ptID, numVar, timeVar)


uwLineGraph(
  data = df,
  metricName = "numVar",
  trxName = "TRT",
  factorName = "timeVar",
  LatexFileName = NULL,
  plotMean = TRUE,
  pch = NULL,
  colScale = TRUE,
  yLim = NULL,
  yLab = "",
  xLab = "",
  pTitle = "Example of uwLineGraph",
  refLines = TRUE,
  Legend = TRUE,
  LegendLoc = "topright",
  printPVals = TRUE,
  pTest = "t",
  pExclude = NULL,
  trxControl = "A",
  pairDiffTab = TRUE,
  ptIDname = "ptID",
  BaseLevel = "Baseline",
  numDec = 2,
  rowLines = list(c(FALSE), c(FALSE)),
  caption = list(c(NULL), c(NULL)),
  firstCol.name = "Time",
  Ropen = FALSE
)

jbirstler/biostatrpts documentation built on May 7, 2020, 12:10 a.m.