hGraph: Create multiplicity graphs using ggplot2

In allenzhuaz/gMCPmini: Graph Based Multiple Comparison Procedures (Minimized Version without Java Dependency)

Create multiplicity graphs using ggplot2

Description

Plots a multiplicity graph defined by user inputs. The graph can also be used with the ***gMCP*** package to evaluate a set of nominal p-values for the tests of the hypotheses in the graph.

Usage

hGraph(
  nHypotheses = 4,
  nameHypotheses = paste("H", (1:nHypotheses), sep = ""),
  alphaHypotheses = 0.025/nHypotheses,
  m = matrix(array(1/(nHypotheses - 1), nHypotheses^2), nrow = nHypotheses) -
    diag(1/(nHypotheses - 1), nHypotheses),
  fill = 1,
  palette = grDevices::gray.colors(length(unique(fill)), start = 0.5, end = 0.8),
  labels = LETTERS[1:length(unique(fill))],
  legend.name = " ",
  legend.position = "none",
  halfWid = 0.5,
  halfHgt = 0.5,
  trhw = 0.1,
  trhh = 0.075,
  trprop = 1/3,
  digits = 5,
  trdigits = 2,
  size = 6,
  boxtextsize = 4,
  legend.textsize = size * 2.5,
  arrowsize = 0.02,
  radianStart = if ((nHypotheses)%%2 != 0) {
     pi * (1/2 + 1/nHypotheses)
 } else
    {
     pi * (1 + 2/nHypotheses)/2
 },
  offset = pi/4/nHypotheses,
  xradius = 2,
  yradius = xradius,
  x = NULL,
  y = NULL,
  wchar = "\u03b1"
)

Arguments

nHypotheses	number of hypotheses in graph
nameHypotheses	hypothesis names
alphaHypotheses	alpha-levels or weights for ellipses
m	square transition matrix of dimension 'nHypotheses'
fill	grouping variable for hypotheses
palette	colors for groups
labels	text labels for groups
legend.name	text for legend header
legend.position	text string or x,y coordinates for legend
halfWid	half width of ellipses
halfHgt	half height of ellipses
trhw	transition box width
trhh	transition box height
trprop	proportion of transition arrow length where transition box is placed
digits	number of digits to show for alphaHypotheses
trdigits	digits displayed for transition weights
size	text size in ellipses
boxtextsize	transition text size
legend.textsize	legend text size
arrowsize	size of arrowhead for transition arrows
radianStart	radians from origin for first ellipse; nodes spaced equally in clockwise order with centers on an ellipse by default
offset	rotational offset in radians for transition weight arrows
xradius	horizontal ellipse diameter on which ellipses are drawn
yradius	vertical ellipse diameter on which ellipses are drawn
x	x coordinates for hypothesis ellipses if elliptical arrangement is not wanted
y	y coordinates for hypothesis ellipses if elliptical arrangement is not wanted
wchar	character for alphaHypotheses in ellipses; defaults to the Unicode escape sequence \u03b1 (Greek letter alpha). See list of Unicode characters for a more comprehensive character list.

Details

See vignette **Multiplicity graphs formatting using ggplot2** for explanation of formatting.

Value

A 'ggplot' object with a multi-layer multiplicity graph

Examples

# Defaults: note clockwise ordering
hGraph(5)
# Add colors (default is 3 gray shades)
hGraph(3,fill=1:3)
# Colorblind palette
cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73",
               "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
hGraph(6,fill=as.factor(1:6),palette=cbPalette)
# Use a hue palette
hGraph(4,fill=factor(1:4),palette=scales::hue_pal(l=75)(4))
# different alpha allocation, hypothesis names and transitions
alphaHypotheses <- c(.005,.007,.013)
nameHypotheses <- c("ORR","PFS","OS")
m <- matrix(c(0,1,0,
              0,0,1,
              1,0,0),nrow=3,byrow=TRUE)
hGraph(3,alphaHypotheses=alphaHypotheses,nameHypotheses=nameHypotheses,m=m)
# Custom position and size of ellipses, change text to multi-line text
# Adjust box width
# add legend in middle of plot
hGraph(3,x=sqrt(0:2),y=c(1,3,1.5),size=6,halfWid=.3,halfHgt=.3, trhw=0.6,
       palette=cbPalette[2:4], fill = c(1, 2, 2),
       legend.position = c(.6,.5), legend.name = "Legend:", labels = c("Group 1", "Group 2"),
       nameHypotheses=c("H1:\n Long name","H2:\n Longer name","H3:\n Longest name"))

allenzhuaz/gMCPmini documentation built on Sept. 3, 2022, 10:27 a.m.