ps_2dPlot: ps_2dPlot

In benmarwick/karon: Compositional Data Analysis of Archaeological Artefacts

ps_2dPlot

Description

Create 2-dimensional scatter plots, using ps_plot().

Usage

ps_2dPlot(
  doc = "ps_2dPlot",
  data,
  GroupVar,
  AnalyticVars,
  ID = "none",
  Groups,
  ByGroup = FALSE,
  PlotAllGroups = FALSE,
  VariablePairs,
  PlotPoints = TRUE,
  LowessLine = TRUE,
  Lowess_f = NA,
  PlotMedians = FALSE,
  PlotEllipses = FALSE,
  Ellipses = c(0.95, 0.99),
  KernelSmooth = FALSE,
  Kernelwidth = 0.3,
  PlotHulls = FALSE,
  parRowsCols = c(2, 2),
  Colors = c("red", "black", "blue", "green", "purple"),
  legendLoc = "topleft",
  Identify = FALSE
)

Arguments

doc	A string documenting use written to the output list; default is the function name
data	A data frame containing the data to be analyzed
GroupVar	The name for the variable defining grouping; can be " " if no grouping
AnalyticVars	The names of analytic variables to be used
ID	The character value of the name of a lab ID, "none" (the default) if none
Groups	A vector of values of GroupVar for which plots are to be done; if "All", use all groups; if " ", no grouping
ByGroup	Logical. If TRUE, show scatterplot for each group for each selection of 2 variables; if FALSE (the default), all specified groups are on one plot
PlotAllGroups	Logical. If TRUE (default is FALSE), all groups are one one plot, with group membership shown. If PlotEllipses is TRUE, confidence ellipses are also shown.
VariablePairs	The names of two analytic variables to be shown in the plots, vector of length 2 or matrix with 2 columns; if a matrix, the set of plots is produced for each row.
PlotPoints	Logical. If TRUE (the default), all points are plotted; if FALSE, no points are plotted
LowessLine	Logical. If TRUE, a lowess line is plotted for each group; if FALSE, no line is plotted
Lowess_f	A parameter for lowess() less than or equal to 1, defining the range of x-values used; if NA (the default), uses the default value of 0.67
PlotMedians	if TRUE, the code for each group is plotted at the median of the values for that group; default is FALSE
PlotEllipses	Logical. If TRUE, Gaussian confidence ellipses are plotted for each group; if F (the default), no ellipses are plotted
Ellipses	single value or vector of values with confidence values for the ellipses; default is c(0.95,0.99)
KernelSmooth	Logical. If TRUE, a kernel smooth is plotted for each group; if FALSE (the default), no kernel smooth is plotted
Kernelwidth	the proportion of the range of x-values used in the kernel smooth; default is 0.3
PlotHulls	if TRUE, the convex hull is drawn for each set of points; if FALSE (the default), no hulls are drawn
parRowsCols	A vector of length 2, with the numbers of rows and columns for a plot when plots are shown by group; default is c(2,2)
Colors	A vector with the colors of plotted points, used sequentially for the groups
legendLoc	Character. Identifies the location of the legend for a plot showing all groups on one plot. Default is "topleft"; alternatives are "bottomleft", "topright", "bottomright"
Identify	if TRUE, user can identify points of interest in the plots; default is FALSE

Value

• usage: A string with the contents of the argument doc, the date run, the version of R used

• dataUsed: The contents of the argument data restricted to the groups used

• dataNA: A data frame with observations containing at least one missing value for an analysis variable, NA if no missing values

• params: A list with the values of the grouping, logical, numeric and Color arguments

• analyticVars: A vector with the value of the argument AnalyticVars

• dataCheck: If ps_identify = TRUE, a data frame with the information on user-identified points of interest

Details

With multiple plots, execution halts after each page is complete; enter c (continue) at the prompt to continue execution. For a plot of the labelled convex hulls of the groups, see the example code for the required combination of logical arguments.

Examples

# All Jemez obsidian sources on one plot
data(ObsidianSources)
analyticVars<-c("Rb","Nb","Zr","Y","Sr")
temp<-ps_2dPlot(data=ObsidianSources,GroupVar="Code",Groups="All",ByGroup=FALSE,
AnalyticVars=analyticVars,VariablePairs=c("Rb","Nb"),PlotEllipses=TRUE,PlotAllGroups=TRUE)

# Plots of obsidian source data for each source with confidence ellipses and lowess lines
data(ObsidianSources)
analyticVars<-c("Rb","Nb","Zr","Y","Sr")
temp<-ps_2dPlot(data=ObsidianSources,GroupVar="Code",Groups="All",ByGroup=TRUE,
AnalyticVars=analyticVars,VariablePairs=c("Rb","Nb"),PlotEllipses=TRUE,PlotAllGroups=FALSE)

# Plot of the labelled convex hulls of the obsidian source data for each source
data(ObsidianSources)
analyticVars<-c("Rb","Nb","Zr","Y","Sr")
temp<-ps_2dPlot(data=ObsidianSources,GroupVar="Code",Groups="All",ByGroup=FALSE,
AnalyticVars=analyticVars,VariablePairs=c("Rb","Nb"),PlotEllipses=FALSE,LowessLine=FALSE,
PlotHulls=TRUE,PlotMedians=TRUE,PlotPoints=FALSE)

benmarwick/karon documentation built on July 29, 2023, 10:11 a.m.