Package 'figuRes2' reference manual

Title:	Support for a Variety of Figure Production Tasks
Description:	We view a figure as a collection of graphs/tables assembled on a page and optionally annotated with metadata (titles, headers and footers). Functions and supporting documentation are offered to streamline a variety of figure production task.
Authors:	Greg Cicconetti [aut, cre] , David Wade [aut]
Maintainer:	Greg Cicconetti <[email protected]>
License:	GPL-2
Version:	1.0.0
Built:	2024-10-30 03:46:03 UTC
Source:	https://github.com/gcicc/figures2

all_in_one

Description

Produces a single pdf file with based on rows in the outputplan whose UseSubset column is equals 'Y'. A progress bar is displayed.

Usage

all_in_one(UseSubset = "SAC", filename = "SAC.pdf", reportNR = TRUE)
all_in_one(UseSubset = "SAC", filename = "SAC.pdf", reportNR = TRUE)

Arguments

`UseSubset`	Corresponds to a column name in outputplan holding flags (all_in_one)
`filename`	common_root.pdf or common_root.csv
`reportNR`	If TRUE, a plot with missing figure numbers and titles is produced

Details

Prerequisites: You need to have output, code, data directory paths defined in your workspace. These should take variable names od, cd, dd, respectively. This can be done by running a personalized set of the following commands:

Code directory needs to hold the .r files associated with the subset of figures to be produced.

Suggest running outputplan.report() first. A progress bar also helps to see run is incomplete. A manual check on the total number of pages in the final pdf should be made.

Value

A .pdf file called filename.pdf is deposited in the output directory.

Author(s)

Greg Cicconetti

annotate.page

Description

Optionally adds up to 4 lines for titles, 3 lines for right and left headers, and 5 lines of footnotes

Usage

annotate.page(
  page.height = 8.5,
  page.width = 11,
  top.margin = 1 - 0.5,
  bottom.margin = 1 - 0.5,
  right.margin = 0.75,
  left.margin = 0.75,
  foot.size = 10,
  head.size = 10,
  title.size = 14,
  add.fignum = TRUE,
  fnote.buffer = 0,
  header.buffer = 0,
  fignum.buffer = 1,
  title.buffer = 2,
  fignum = "1.100",
  title = list("If ggplot populates title, annotate.page's title argument gets a ",
    "list of whitespace text strings. If annotate.page is populating titles,",
    "use whitespaces and newline escape characters in ggplot titles",
    "to ensure ggplot object is shrunken titles do not stamp over your graphs"),
  ulh = list("Upper Left Header 1", "Upper Left Header 2", "Upper Left Header 3"),
  urh = list("Upper Right Header 1", "Upper Right Header 2", "Upper Right Header 3"),
  fnote = list("Footnote1: Up to five lines of footnotes can be annotated.",
    "Footnote2: Graphic region height can be flexed.", "Footnote3", "Footnote4",
    "Footnote5: In large-scale production, this may hold file name, time stamp, etc."),
  override = "",
  addTime = TRUE
)
annotate.page(
  page.height = 8.5,
  page.width = 11,
  top.margin = 1 - 0.5,
  bottom.margin = 1 - 0.5,
  right.margin = 0.75,
  left.margin = 0.75,
  foot.size = 10,
  head.size = 10,
  title.size = 14,
  add.fignum = TRUE,
  fnote.buffer = 0,
  header.buffer = 0,
  fignum.buffer = 1,
  title.buffer = 2,
  fignum = "1.100",
  title = list("If ggplot populates title, annotate.page's title argument gets a ",
    "list of whitespace text strings. If annotate.page is populating titles,",
    "use whitespaces and newline escape characters in ggplot titles",
    "to ensure ggplot object is shrunken titles do not stamp over your graphs"),
  ulh = list("Upper Left Header 1", "Upper Left Header 2", "Upper Left Header 3"),
  urh = list("Upper Right Header 1", "Upper Right Header 2", "Upper Right Header 3"),
  fnote = list("Footnote1: Up to five lines of footnotes can be annotated.",
    "Footnote2: Graphic region height can be flexed.", "Footnote3", "Footnote4",
    "Footnote5: In large-scale production, this may hold file name, time stamp, etc."),
  override = "",
  addTime = TRUE
)

Arguments

`page.height`	used by build.page and annotate.page; presumed to be inches
`page.width`	used by build.page and annotate.page; presumed to be inches
`top.margin`	used by build.page and annotate.page; presumed to be inches
`bottom.margin`	used by build.page and annotate.page
`right.margin`	used by build.page and annotate.page; presumed to be inches
`left.margin`	used by build.page and annotate.page; presumed to be inches
`foot.size`	default: 10; passed to grid.text via gp (annotate.page)
`head.size`	default: 10 (anotate.page)
`title.size`	default: 14; passed to grid.text via gp (annotate.page)
`add.fignum`	logical (annotate.page)
`fnote.buffer`	fine-control of vertical position (annotate.page)
`header.buffer`	fine-control of vertical position (anotate.page)
`fignum.buffer`	fine-control of vertical position (annotate.page)
`title.buffer`	fine-control of vertical position (annotate.page)
`fignum`	figure number (annotate.page)
`title`	vector of title lines (annotate.page)
`ulh`	vector for upper left headers (annotate.page)
`urh`	vector for upper right headers (annotate.page)
`fnote`	vector of 5 footnotes. 5th row is traditionally reserved for filepath, table reference and time stamp. Populate from bottom up. (annotate.page)
`override`	override
`addTime`	logical for ading time stamp (annotate.page)

Value

Following an application of build.page, this function stamps on meta-data.

Author(s)

Greg Cicconetti

bar.plot

Description

A function for creating harmonized ggplot2 bar charts

Usage

bar.plot(
  parent.df,
  category.col = "TRTGRP",
  category.label = "Treatment Group",
  x.label = "",
  y.col = "GWHRT",
  y.label = "Percentage of Subjects",
  y.limits = c(0, 0.7),
  y.ticks = seq(0, 0.3, 0.05),
  bar.position = "dodge",
  category.palette = c("red", "blue"),
  text.size = 3,
  text.buffer = 0.05,
  killMissing = TRUE
)
bar.plot(
  parent.df,
  category.col = "TRTGRP",
  category.label = "Treatment Group",
  x.label = "",
  y.col = "GWHRT",
  y.label = "Percentage of Subjects",
  y.limits = c(0, 0.7),
  y.ticks = seq(0, 0.3, 0.05),
  bar.position = "dodge",
  category.palette = c("red", "blue"),
  text.size = 3,
  text.buffer = 0.05,
  killMissing = TRUE
)

Arguments

`parent.df`	data.frame used by ggplot
`category.col`	data.frame column associated with categorical variable (bar.plot, box.plot, cdf.plot, dot.plot, km.plot)
`category.label`	passed to x-axis label
`x.label`	value gets passed to labs
`y.col`	parent.df column associated with response vairable
`y.label`	value gets passed to labs
`y.limits`	passed to scale_y_continuous
`y.ticks`	passed to scale_y_continuous
`bar.position`	passed to geom_bar (bar.plot)
`category.palette`	colors assoicated with categorical variable
`text.size`	value gets passed to geom_text
`text.buffer`	used by bar.plot to control text placement
`killMissing`	logical used by bar.plot

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

Examples

{
# Access dummy demography dataset
data(demog.data)
levels(demog.data$SEX) <- c("Female", "Male")

# A ggplot object is returned
p1 <- bar.plot(parent.df = demog.data, y.col = "SEX", 
x.label= "Gender", y.label = "Percentage of Subjects", 
category.col = "REGION", category.label = "Region", 
y.limits = c(0, 0.35), y.ticks = seq(0, 0.5, 0.05), 
bar.position= "dodge", 
category.palette = RColorBrewer::brewer.pal(n=5, name = "Dark2"),
text.size =4, text.buffer=.025, killMissing = TRUE) 
print(p1)
} 
{
# Access dummy demography dataset
data(demog.data)
levels(demog.data$SEX) <- c("Female", "Male")

# A ggplot object is returned
p1 <- bar.plot(parent.df = demog.data, y.col = "SEX", 
x.label= "Gender", y.label = "Percentage of Subjects", 
category.col = "REGION", category.label = "Region", 
y.limits = c(0, 0.35), y.ticks = seq(0, 0.5, 0.05), 
bar.position= "dodge", 
category.palette = RColorBrewer::brewer.pal(n=5, name = "Dark2"),
text.size =4, text.buffer=.025, killMissing = TRUE) 
print(p1)
}

This is a dataset structured for building figures using forest.plot

Description

This is a dataset structured for building figures using forest.plot

Author(s)

Greg Cicconetti

box.plot

Description

A function for creating harmonized ggplot2 boxplots

Usage

box.plot(
  parent.df,
  y.col = "AGE",
  y.label = "AGE",
  category.col = "TRTGRP",
  category.label = "Treatment Group",
  y.limits = NULL,
  y.ticks = NULL,
  y.digits = 0,
  shape.palette = c(21, 22),
  category.palette = c(2, 3),
  text.size = 4
)
box.plot(
  parent.df,
  y.col = "AGE",
  y.label = "AGE",
  category.col = "TRTGRP",
  category.label = "Treatment Group",
  y.limits = NULL,
  y.ticks = NULL,
  y.digits = 0,
  shape.palette = c(21, 22),
  category.palette = c(2, 3),
  text.size = 4
)

Arguments

`parent.df`	data.frame used by ggplot
`y.col`	parent.df column associated with response vairable
`y.label`	value gets passed to labs
`category.col`	data.frame column associated with categorical variable (bar.plot, box.plot, cdf.plot, dot.plot, km.plot)
`category.label`	passed to x-axis label
`y.limits`	passed to scale_y_continuous
`y.ticks`	passed to scale_y_continuous
`y.digits`	passed to scale_y_continuous label's, fmt (box.plot, line.plot)
`shape.palette`	values passed to scale_shape_manual
`category.palette`	colors assoicated with categorical variable
`text.size`	value gets passed to geom_text

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

Examples

{
data(demog.data)
# pre-processing

levels(demog.data$SEX) <- c("Female", "Male")

 p1 <- box.plot(parent.df = demog.data, 
     y.col = "BMI", 
     y.label = expression(paste("BMI (m/kg",phantom()^2,")")), 
     category.col = "SEX",
     category.label = "Gender", 
      y.limits = c(0, 70), 
      y.ticks = seq(0, 100, 10), 
      y.digits = 0,
      shape.palette = c(20, 20),
      category.palette = rainbow(6),
      text.size = 4)
 print(p1)
}
{
data(demog.data)
# pre-processing

levels(demog.data$SEX) <- c("Female", "Male")

 p1 <- box.plot(parent.df = demog.data, 
     y.col = "BMI", 
     y.label = expression(paste("BMI (m/kg",phantom()^2,")")), 
     category.col = "SEX",
     category.label = "Gender", 
      y.limits = c(0, 70), 
      y.ticks = seq(0, 100, 10), 
      y.digits = 0,
      shape.palette = c(20, 20),
      category.palette = rainbow(6),
      text.size = 4)
 print(p1)
}

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

build.page

Description

Takes page dimensions, figure layout dimensions and an ordered list of grobs/ggplot objects orients them on a page

Usage

build.page(
  interior.h = c(1),
  interior.w = c(1),
  ncol = 1,
  nrow = 1,
  interior,
  test.dim = FALSE,
  page.height = 8.5,
  page.width = 11,
  right.margin = 0.75,
  left.margin = 0.75,
  top.margin = 1.4 - 0.5,
  bottom.margin = 1.75 - 0.5,
  pos = 1,
  envir = as.environment(pos)
)
build.page(
  interior.h = c(1),
  interior.w = c(1),
  ncol = 1,
  nrow = 1,
  interior,
  test.dim = FALSE,
  page.height = 8.5,
  page.width = 11,
  right.margin = 0.75,
  left.margin = 0.75,
  top.margin = 1.4 - 0.5,
  bottom.margin = 1.75 - 0.5,
  pos = 1,
  envir = as.environment(pos)
)

Arguments

`interior.h`	a vector summing to 1 to indicate how to partition the heights (build.page)
`interior.w`	a vector summing to 1 to indicate how to partition the widths (build.page)
`ncol`	number of columns for the grid of graphics being built by build.page
`nrow`	number of rows for the grid of graphics being built by build.page
`interior`	a list of nrow*ncol grobs/ggplot objects to be displayed in the grid, ordered by row then col (build.page)
`test.dim`	logical. Assists with figure development. If TRUE it makes a call to grid.show.layout.
`page.height`	used by build.page and annotate.page; presumed to be inches
`page.width`	used by build.page and annotate.page; presumed to be inches
`right.margin`	used by build.page and annotate.page; presumed to be inches
`left.margin`	used by build.page and annotate.page; presumed to be inches
`top.margin`	used by build.page and annotate.page; presumed to be inches
`bottom.margin`	used by build.page and annotate.page
`pos`	used internally by some functions
`envir`	used internally by some functions

Value

This writes graphics/grobs to a device.

Author(s)

Greg Cicconetti

Examples

{
# Commenting out calls to pdf and dev.off.
# pdf(file = "demonstrating build.page.pdf", width = 11, height = 8.5)
build.page(test.dim= TRUE)
build.page(interior.w = c(.5, .5), ncol=2, nrow=1, test.dim= TRUE)
build.page(interior.h = c(.5, .5), ncol=1, nrow=2, test.dim= TRUE)
build.page(interior.h = c(.5, .5), interior.w = c(.5, .5), ncol=2, nrow=2, test.dim= TRUE)
build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(1),
           ncol=1, nrow=3,
           test.dim=TRUE)
build.page(interior.h=c(2, 1, 3)/6,
           interior.w=c(.6, .4),
           ncol=2, nrow=3,
           test.dim=TRUE)
build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(.5, .5),
           ncol=2, nrow=3,
           test.dim=TRUE,
           top.margin=.1,
           bottom.margin=.1,
           right.margin=.1,
           left.margin=.1)

parabola.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()
parabola.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()
cubic.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()
cubic.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()

red.parabola.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")
red.parabola.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")
red.cubic.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")
red.cubic.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")



build.page(interior.h = c(.5, .5), nrow=2, ncol=1,
           test.dim= FALSE, interior = list(parabola.up, 
                                       parabola.down))

build.page(interior.w = c(.5, .5), nrow=1, ncol=2,
           test.dim= FALSE, interior = list(parabola.up, 
                                       parabola.down))

build.page(interior.w = c(.5, .5), interior.h = c(.5, .5), nrow=2, ncol=2,
           test.dim= FALSE, interior = list(parabola.up, 
                                       red.parabola.up,
                                       parabola.down, 
                                       red.parabola.down
                                       ))

build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(1),
           ncol=1, nrow=3,
           interior = list(parabola.up, 
                           parabola.down,
                           cubic.up
           ))

build.page(interior.w=c(1/3,1/3,1/3),
           interior.h=c(1),
           ncol=3, nrow=1,
           interior = list(parabola.up, 
                           parabola.down,
                           cubic.up
           ))

build.page(interior.h=c(2, 1, 3)/6,
           interior.w=c(.6, .4),
           ncol=2, nrow=3,
           interior = list(parabola.up, 
                parabola.down,
                cubic.up,
                cubic.down, 
                red.parabola.down,
                red.cubic.down)
           )

build.page(interior.h=c(1/3, 1/3, 1/3),
           interior.w=c(.5, .5),
           ncol=2, nrow=3,
           interior = list(parabola.up,
                           parabola.down,
                           cubic.up,
                           cubic.down, 
                           red.parabola.down,
                           red.cubic.down)
)


build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(.5, .5),
           ncol=2, nrow=3,
           top.margin=.1,
           bottom.margin=.1,
           right.margin=.1,
           left.margin=.1,
           interior = list(parabola.up,
                           parabola.down,
                           cubic.up,
                           cubic.down, 
                           red.parabola.down,
                           red.cubic.down))


# dev.off()

} 
{
# Commenting out calls to pdf and dev.off.
# pdf(file = "demonstrating build.page.pdf", width = 11, height = 8.5)
build.page(test.dim= TRUE)
build.page(interior.w = c(.5, .5), ncol=2, nrow=1, test.dim= TRUE)
build.page(interior.h = c(.5, .5), ncol=1, nrow=2, test.dim= TRUE)
build.page(interior.h = c(.5, .5), interior.w = c(.5, .5), ncol=2, nrow=2, test.dim= TRUE)
build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(1),
           ncol=1, nrow=3,
           test.dim=TRUE)
build.page(interior.h=c(2, 1, 3)/6,
           interior.w=c(.6, .4),
           ncol=2, nrow=3,
           test.dim=TRUE)
build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(.5, .5),
           ncol=2, nrow=3,
           test.dim=TRUE,
           top.margin=.1,
           bottom.margin=.1,
           right.margin=.1,
           left.margin=.1)

parabola.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()
parabola.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()
cubic.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()
cubic.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line()

red.parabola.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")
red.parabola.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^2), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")
red.cubic.up <- ggplot2::ggplot(data.frame(x=-10:10, y=(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")
red.cubic.down <- ggplot2::ggplot(data.frame(x=-10:10, y=-(-10:10)^3), ggplot2::aes(x=x,y=y))+
ggplot2::geom_line(color="red")



build.page(interior.h = c(.5, .5), nrow=2, ncol=1,
           test.dim= FALSE, interior = list(parabola.up, 
                                       parabola.down))

build.page(interior.w = c(.5, .5), nrow=1, ncol=2,
           test.dim= FALSE, interior = list(parabola.up, 
                                       parabola.down))

build.page(interior.w = c(.5, .5), interior.h = c(.5, .5), nrow=2, ncol=2,
           test.dim= FALSE, interior = list(parabola.up, 
                                       red.parabola.up,
                                       parabola.down, 
                                       red.parabola.down
                                       ))

build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(1),
           ncol=1, nrow=3,
           interior = list(parabola.up, 
                           parabola.down,
                           cubic.up
           ))

build.page(interior.w=c(1/3,1/3,1/3),
           interior.h=c(1),
           ncol=3, nrow=1,
           interior = list(parabola.up, 
                           parabola.down,
                           cubic.up
           ))

build.page(interior.h=c(2, 1, 3)/6,
           interior.w=c(.6, .4),
           ncol=2, nrow=3,
           interior = list(parabola.up, 
                parabola.down,
                cubic.up,
                cubic.down, 
                red.parabola.down,
                red.cubic.down)
           )

build.page(interior.h=c(1/3, 1/3, 1/3),
           interior.w=c(.5, .5),
           ncol=2, nrow=3,
           interior = list(parabola.up,
                           parabola.down,
                           cubic.up,
                           cubic.down, 
                           red.parabola.down,
                           red.cubic.down)
)


build.page(interior.h=c(1/3,1/3,1/3),
           interior.w=c(.5, .5),
           ncol=2, nrow=3,
           top.margin=.1,
           bottom.margin=.1,
           right.margin=.1,
           left.margin=.1,
           interior = list(parabola.up,
                           parabola.down,
                           cubic.up,
                           cubic.down, 
                           red.parabola.down,
                           red.cubic.down))


# dev.off()

}

This is a dataset that would need some pre-processing ahead of using line.plot

Description

This is a dataset that would need some pre-processing ahead of using line.plot

Author(s)

Greg Cicconetti

This is a dataset structured for building figures using cdf.plot

Description

This is a dataset structured for building figures using cdf.plot

Author(s)

Greg Cicconetti

cdf.plot

Description

A function for creating harmonized ggplot2 cumulative distribution plots. Statistics computed by stat_ecdf().

Usage

cdf.plot(
  parent.df,
  category.col,
  category.label,
  response.col,
  x.label = "",
  x.limits = NULL,
  x.ticks = NULL,
  y.label = "",
  y.limits = c(0, 1),
  y.ticks = seq(0, 1, 0.2),
  line.size = 0.75,
  category.palette = c("red", "blue")
)
cdf.plot(
  parent.df,
  category.col,
  category.label,
  response.col,
  x.label = "",
  x.limits = NULL,
  x.ticks = NULL,
  y.label = "",
  y.limits = c(0, 1),
  y.ticks = seq(0, 1, 0.2),
  line.size = 0.75,
  category.palette = c("red", "blue")
)

Arguments

`parent.df`	data.frame used by ggplot
`category.col`	data.frame column associated with categorical variable (bar.plot, box.plot, cdf.plot, dot.plot, km.plot)
`category.label`	passed to x-axis label
`response.col`	used by cdf.plottttt
`x.label`	value gets passed to labs
`x.limits`	value gets passed to scale_x_continuous
`x.ticks`	value gets passed to scale_x_continuous
`y.label`	value gets passed to labs
`y.limits`	passed to scale_y_continuous
`y.ticks`	passed to scale_y_continuous
`line.size`	value gets passed to size within geom_line, geom_step
`category.palette`	colors assoicated with categorical variable

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

Examples

{
data(demog.data)
cdf.plot(parent.df= demog.data, 
  category.col = "SEX",
  category.label   = "Gender",
  response.col = "BMI", 
  x.label = expression(paste("BMI (m/kg",phantom()^2,")")), 
  x.limits=c(0,60),
  x.ticks=seq(0,60,5),
  y.label = "Percentage of Subjects", 
  y.limits= c(0,1),
  y.ticks = seq(0,1,.2),
  line.size =.75,
  category.palette =c("red", "blue")
  )
}
{
data(demog.data)
cdf.plot(parent.df= demog.data, 
  category.col = "SEX",
  category.label   = "Gender",
  response.col = "BMI", 
  x.label = expression(paste("BMI (m/kg",phantom()^2,")")), 
  x.limits=c(0,60),
  x.ticks=seq(0,60,5),
  y.label = "Percentage of Subjects", 
  y.limits= c(0,1),
  y.ticks = seq(0,1,.2),
  line.size =.75,
  category.palette =c("red", "blue")
  )
}

check.ggplot.outliers

Description

Reports via cat statements when ggplot windows truncate data

Usage

check.ggplot.outliers(plot.object = NULL)
check.ggplot.outliers(plot.object = NULL)

Arguments

plot.object

the ggplot object to check

Details

Used in conjunction with log files created with start_session_log

Author(s)

David Wade

default.settings

Description

Global Defaults

Usage

default.settings(
  pos = 1,
  envir = as.environment(pos),
  my.path = getwd(),
  main.theme = "theme_bw",
  page.width = 11,
  page.height = 8.5,
  right.margin = 0.75,
  left.margin = 0.75,
  top.margin = 1.4 - 0.5,
  bottom.margin = 1.75 - 0.5
)
default.settings(
  pos = 1,
  envir = as.environment(pos),
  my.path = getwd(),
  main.theme = "theme_bw",
  page.width = 11,
  page.height = 8.5,
  right.margin = 0.75,
  left.margin = 0.75,
  top.margin = 1.4 - 0.5,
  bottom.margin = 1.75 - 0.5
)

Arguments

`pos`	used internally by some functions
`envir`	used internally by some functions
`my.path`	path to main directory,
`main.theme`	text string name of theme to be called by theme_set,
`page.width`	used by build.page and annotate.page; presumed to be inches
`page.height`	used by build.page and annotate.page; presumed to be inches
`right.margin`	used by build.page and annotate.page; presumed to be inches
`left.margin`	used by build.page and annotate.page; presumed to be inches
`top.margin`	used by build.page and annotate.page; presumed to be inches
`bottom.margin`	used by build.page and annotate.page

Details

Global Defaults

Value

The following are assigned to global environment upon calling:

my.path
dd
cd
od
blankPanel
page.width
page.height
right.margin
left.margin
top.margin
bottom.margin
graph.region.h
graph.region.w

Author(s)

Greg Cicconetti

This is a dataset structured for building figures using bar.plot, box.plot, and cdf.plot

Description

This is a dataset structured for building figures using bar.plot, box.plot, and cdf.plot

Author(s)

Greg Cicconetti

dot.plot

Description

A function for creating harmonized ggplot2 dot plots with compatiability with table.plot and forest.plot.

Usage

dot.plot(
  parent.df = dot.df.melt,
  category.col = "Treatment",
  y.rank.col = "rank",
  y.label.rank.col = "label.rank",
  y.label.col = "subgroup",
  Point.Est = "percent",
  x.limits = c(0, 1),
  x.ticks = seq(0, 1, 0.2),
  y.limits = NULL,
  shape.palette = c(16, 17),
  x.label = "Estimate",
  y.label = "Item",
  category.palette = c("red", "blue")
)
dot.plot(
  parent.df = dot.df.melt,
  category.col = "Treatment",
  y.rank.col = "rank",
  y.label.rank.col = "label.rank",
  y.label.col = "subgroup",
  Point.Est = "percent",
  x.limits = c(0, 1),
  x.ticks = seq(0, 1, 0.2),
  y.limits = NULL,
  shape.palette = c(16, 17),
  x.label = "Estimate",
  y.label = "Item",
  category.palette = c("red", "blue")
)

Arguments

`parent.df`	data.frame used by ggplot
`category.col`	data.frame column associated with categorical variable (bar.plot, box.plot, cdf.plot, dot.plot, km.plot)
`y.rank.col`	column holding ranks for line items in forest/dot/table plots
`y.label.rank.col`	column holding ranks for labels in forest/dot/table plots
`y.label.col`	column holding labels for forest/dot/table plots
`Point.Est`	point estimate
`x.limits`	value gets passed to scale_x_continuous
`x.ticks`	value gets passed to scale_x_continuous
`y.limits`	passed to scale_y_continuous
`shape.palette`	values passed to scale_shape_manual
`x.label`	value gets passed to labs
`y.label`	value gets passed to labs
`category.palette`	colors assoicated with categorical variable

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

This holds lines to a driver file created by the large-scale vignette

Description

This holds lines to a driver file created by the large-scale vignette

Author(s)

Greg Cicconetti

FacetLabelAdjuster

Description

This function takes a 'facet wrapped' ggplot and adds axis labels when a rxc grid is incomplete

Usage

facetAdjust(x, pos = c("up", "down"), newpage = is.null(vp), vp = NULL)
facetAdjust(x, pos = c("up", "down"), newpage = is.null(vp), vp = NULL)

Arguments

`x`	a ggplot object
`pos`	maintain default
`newpage`	maintain default
`vp`	maintain default

References

<http://stackoverflow.com/questions/13297155/add-floating-axis-labels-in-facet-wrap-plot>

figuRes2: A package for building and annotating mult-panel figures with application to large scale figure production

Description

This package takes the view that a figure is a collection of graphs/tables assembled on a page and optionally annotated with metadata (titles, headers and footers). The steps to figure building can then be chunked as follows:

Data importation
Data pre-processing
Graph/table building (with subsequent processing necessary)
Assembling graph/tables on a page
Optional annotation to complete the figure

The figuRes2 package provides a suite of functions for producing harmonized figures using the ggplot2 packages. Additional ggplot themes are included. The package provides functions to assist with assembling multiple graphics on a page and annotating the page with headers and footnotes. Functions to facilitate data processing and mass figure production are included. Data sets are included to demonstrate how the functions work and this document contains a section that walks through the workflow for large scale figure production.

Details

All graphing functions in this package presume a data.frame is supplied with a specific data structure. In practice these can be either imported (e.g., as a .csv file) or generated with R (e.g., output of simulation or call to a probability distirbution function).

Data pre-processing of imported files may be required to ensure the data.frames are organized properly, factors are properly organized and labeled appropriatel, etc. To handle this, the user may wish to author functions to assist with this pre-processing. The demog.data data set and related process.bslchar function provide an example.

The the build.page function is designed to help visualize how graphics are organized on a page, as well as execute the task. The graphics passed to this function can be created with the functions in this package or by the user. With the former, keep in mind that these are merely functions that facilitate the construction of ggplot objects.

In the simplest case a figure will consist of a single graphic.

Some figures call for augmenting a graphic with a table (e.g., forest plots, Kaplan-Meier curves). In these cases, the tables are built using either table.plot or nsubj.plot (or again, the user coded ggplot text table). In the case of Kaplan-Meier curves, it is standard practice to arrange the KM curve on top of a table reporting the Number at Risk. Other figures call for juxtaposing two figures. In these cases, the task is either to arrange 2 graphics in a 1 (row) x 2 (col) or a 2 x 1 grid. More generally, the task is to arrange a dashboard of graphics/tables on an nrow x ncol grid and place them on page with predefined margins.

Once the individual graphs/tables have been created for a figure, pre-processing may be required. E.g., there may be a need to align the y-axes when stacking graphics: if Graph A has the longest y-axis tick label, Graph B will need to be adjusted so graphics are aligned when arranging them on a 2 x 1 grid.

When the collection of graphs/tables have been pre-processed, they can be passed to the build.page function. This function requires the user to specify how the row widths and column heights should be specified as well as the order in which to populate the cells of the grid of graphics.

The defaults presume figures are being displayed on an 8.5 inch x 11 inch page, with landscape orientation and margins of 1.5 inches at the top and bottom and 1 inch margins at the left and right. These dimensions provide sufficient room for 2 lines of headers, 4 lines of footnotes and a effective central region for graphs and tables of size (8.5 - 3) inch x (11 - 2) inch. Generalizing from the defaults is straightforward. Trial and error will be required to fine tune aesthetic aspects.

The function annotate.page has been coded to optionally populate with blank entries (helpful when building graphics that don't require annotation and where margins are minimized), dummy entries (helpful in developement phases) or entries coming from a data.frame called outputplan (helpful for mass figure production).

Author(s)

Greg Cicconetti

fmt

Description

A function to control number of digits used in graphics.

Usage

fmt(digits = 2)
fmt(digits = 2)

Arguments

digits

number of digits displayed

Details

This function is used within ggplot, e.g. (scale_y_continuous(labels=fmt(digits=3))) to control the number of digits presented. By default, axis labels will truncate zeros so that labels might read: 0, 2.5, 5, 7.5. Using this will result in labels: 0.0, 2.5, 5.0, 7.5.

Author(s)

Greg Cicconetti

This is a dataset structured for building figures using forest.plot

Description

This is a dataset structured for building figures using forest.plot

Author(s)

Greg Cicconetti

forest.plot

Description

A function for creating harmonized forest.plots via ggplot2 offering compatiability with table.plot and dot.plot.

Usage

forest.plot(
  parent.df,
  y.rank.col = "rank",
  Point.Est = "hr",
  lower.lim = "low",
  upper.lim = "high",
  y.label.rank.col = "rank",
  y.label.col = "subcategory",
  x.label = "Estimate",
  y.label = "Item",
  log.trans = TRUE,
  x.limits = c(0.21, 5),
  x.ticks = 2^(-2:2),
  y.limits = NULL,
  category.color = "category",
  background.palette = c("red", "blue"),
  category.palette = c("red", "blue"),
  shape.palette = c(16, 16),
  flip.palette = FALSE
)
forest.plot(
  parent.df,
  y.rank.col = "rank",
  Point.Est = "hr",
  lower.lim = "low",
  upper.lim = "high",
  y.label.rank.col = "rank",
  y.label.col = "subcategory",
  x.label = "Estimate",
  y.label = "Item",
  log.trans = TRUE,
  x.limits = c(0.21, 5),
  x.ticks = 2^(-2:2),
  y.limits = NULL,
  category.color = "category",
  background.palette = c("red", "blue"),
  category.palette = c("red", "blue"),
  shape.palette = c(16, 16),
  flip.palette = FALSE
)

Arguments

`parent.df`	data.frame used by ggplot
`y.rank.col`	column holding ranks for line items in forest/dot/table plots
`Point.Est`	point estimate
`lower.lim`	column holding lower limit of CI
`upper.lim`	column holding upper limit of CI (forest.plot)
`y.label.rank.col`	column holding ranks for labels in forest/dot/table plots
`y.label.col`	column holding labels for forest/dot/table plots
`x.label`	value gets passed to labs
`y.label`	value gets passed to labs
`log.trans`	Logical; if TRUE log transformation is applied to x axis (ensure x.limits are positive!) (forest.plot)
`x.limits`	value gets passed to scale_x_continuous
`x.ticks`	value gets passed to scale_x_continuous
`y.limits`	passed to scale_y_continuous
`category.color`	data.frame column assocated with aes color mapping (forest.plot, line.plot, nsubj.plot, table.plot)
`background.palette`	palette gets passed to scale_fill_manual (forest.plot)
`category.palette`	colors assoicated with categorical variable
`shape.palette`	values passed to scale_shape_manual
`flip.palette`	logical; if TRUE it reverse the order of colors used for background (forest.plot)

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

gcurve

Description

A function to exploit base R's curve function. This returns a data.frame holding x and y values returned from a call to curve, but suppress the plotting of that function

Usage

gcurve(
  expr,
  from = NULL,
  to = NULL,
  n = 101,
  add = FALSE,
  type = "l",
  xname = "x",
  xlab = xname,
  ylab = NULL,
  log = NULL,
  xlim = NULL,
  category = NULL,
  ...
)
gcurve(
  expr,
  from = NULL,
  to = NULL,
  n = 101,
  add = FALSE,
  type = "l",
  xname = "x",
  xlab = xname,
  ylab = NULL,
  log = NULL,
  xlim = NULL,
  category = NULL,
  ...
)

Arguments

`expr`	inherited from curve
`from`	inherited from curve
`to`	the range over which the function will be plotted.
`n`	inherited from curve
`add`	inherited from curve
`type`	inherited from curve
`xname`	inherited from curve
`xlab`	inherited from curve
`ylab`	inherited from curve
`log`	inherited from curve
`xlim`	inherited from curve
`category`	option to add a column populated with a factor (by gcurve)
`...`	inherited from curve

Value

A data.frame is returned. Columns include x, y, and optionally category.

Author(s)

Greg Cicconetti

Examples

{
require(ggplot2)
curve(dnorm(x, mean=0, sd=1), from=-4, to = 4, n= 1001)
ggplot(gcurve(expr = dnorm(x, mean=0, sd=1),from=-4, to = 4, n= 1001,
category= "Standard Normal"), aes(x=x, y=y)) + geom_line()
}
{
require(ggplot2)
curve(dnorm(x, mean=0, sd=1), from=-4, to = 4, n= 1001)
ggplot(gcurve(expr = dnorm(x, mean=0, sd=1),from=-4, to = 4, n= 1001,
category= "Standard Normal"), aes(x=x, y=y)) + geom_line()
}

get.top.xaxis

Description

This takes two ggplot objects, steals the bottom x-axis from 2nd object and returns a gtable object with that bottom x-axis per object 1 and top x-axis per object 2

Usage

get.top.xaxis(bottom.axis.version, top.axis.version)
get.top.xaxis(bottom.axis.version, top.axis.version)

Arguments

`bottom.axis.version`	ggplot object with bottom x-axis (get.top.xaxis)
`top.axis.version`	ggplot object with intended top x-axis in bottom position (get.top.xaxis)

Author(s)

Greg Cicconetti

Standard graphics names

Description

This is a dummy function whose purpose is to serve as repository for arguments used by figuRes2 functions.

Usage

graphic.params(
  add.fignum,
  addBars,
  addTime,
  at.risk.palette,
  background.palette,
  bar.position,
  bar.width,
  base_family,
  base_size,
  bottom.axis.version,
  bottom.margin,
  category,
  category.color,
  category.col,
  category.label,
  category.symbol.col,
  category.palette,
  cd,
  censor.col,
  centime.col,
  dd,
  envir,
  fignum,
  fignum.buffer,
  filename,
  flip.palette,
  fnote,
  fnote.buffer,
  foot.size,
  fromthetop,
  gg.list,
  head.size,
  header.buffer,
  interior,
  interior.h,
  interior.w,
  killMissing,
  left.margin,
  linetype.col,
  line.size,
  linetype.palette,
  loadplan,
  logd,
  log.trans,
  lower.lim,
  main.theme,
  my.path,
  ncol,
  nrow,
  nsubj.plot.label,
  od,
  outfile,
  override,
  page.height,
  page.width,
  parent.df,
  pdval,
  Point.Est,
  pos,
  reportNR,
  response.col,
  right.margin,
  shape.label,
  shape.palette,
  source.code,
  text.buffer,
  test.dim,
  text.col,
  text.col1,
  text.col2,
  text.col3,
  text.col4,
  text.size,
  title,
  title.buffer,
  title.size,
  toBMP,
  toEPS,
  toJPEG,
  top.axis.version,
  top.margin,
  toPDF,
  toPNG,
  toWMF,
  ulh,
  upper.lim,
  urh,
  UseSubset,
  x.col,
  x.label,
  x.limits,
  x.ticks,
  x.ticks.labels,
  y.col,
  y.digits,
  y.label,
  y.label.col,
  y.label.rank.col,
  y.limits,
  y.rank.col,
  y.ticks,
  ymax.col,
  ymin.col
)
graphic.params(
  add.fignum,
  addBars,
  addTime,
  at.risk.palette,
  background.palette,
  bar.position,
  bar.width,
  base_family,
  base_size,
  bottom.axis.version,
  bottom.margin,
  category,
  category.color,
  category.col,
  category.label,
  category.symbol.col,
  category.palette,
  cd,
  censor.col,
  centime.col,
  dd,
  envir,
  fignum,
  fignum.buffer,
  filename,
  flip.palette,
  fnote,
  fnote.buffer,
  foot.size,
  fromthetop,
  gg.list,
  head.size,
  header.buffer,
  interior,
  interior.h,
  interior.w,
  killMissing,
  left.margin,
  linetype.col,
  line.size,
  linetype.palette,
  loadplan,
  logd,
  log.trans,
  lower.lim,
  main.theme,
  my.path,
  ncol,
  nrow,
  nsubj.plot.label,
  od,
  outfile,
  override,
  page.height,
  page.width,
  parent.df,
  pdval,
  Point.Est,
  pos,
  reportNR,
  response.col,
  right.margin,
  shape.label,
  shape.palette,
  source.code,
  text.buffer,
  test.dim,
  text.col,
  text.col1,
  text.col2,
  text.col3,
  text.col4,
  text.size,
  title,
  title.buffer,
  title.size,
  toBMP,
  toEPS,
  toJPEG,
  top.axis.version,
  top.margin,
  toPDF,
  toPNG,
  toWMF,
  ulh,
  upper.lim,
  urh,
  UseSubset,
  x.col,
  x.label,
  x.limits,
  x.ticks,
  x.ticks.labels,
  y.col,
  y.digits,
  y.label,
  y.label.col,
  y.label.rank.col,
  y.limits,
  y.rank.col,
  y.ticks,
  ymax.col,
  ymin.col
)

Arguments

`add.fignum`	logical (annotate.page)
`addBars`	logical to add error bars (line.plot)
`addTime`	logical for ading time stamp (annotate.page)
`at.risk.palette`	colors to be assocated with categorical variable in accompanying km.plot generated at.risk table
`background.palette`	palette gets passed to scale_fill_manual (forest.plot)
`bar.position`	passed to geom_bar (bar.plot)
`bar.width`	used by line.plot
`base_family`	used in set_theme calls
`base_size`	used in set_theme calls
`bottom.axis.version`	ggplot object with bottom x-axis (get.top.xaxis)
`bottom.margin`	used by build.page and annotate.page
`category`	option to add a column populated with a factor (by gcurve)
`category.color`	data.frame column assocated with aes color mapping (forest.plot, line.plot, nsubj.plot, table.plot)
`category.col`	data.frame column associated with categorical variable (bar.plot, box.plot, cdf.plot, dot.plot, km.plot)
`category.label`	passed to x-axis label
`category.symbol.col`	used by line.plot
`category.palette`	colors assoicated with categorical variable
`cd`	directory where driver (code) files are stored
`censor.col`	name of parent.df column associated with censor variable
`centime.col`	name of parent.df column associated with censored time
`dd`	directory where data is stored
`envir`	used internally by some functions
`fignum`	figure number (annotate.page)
`fignum.buffer`	fine-control of vertical position (annotate.page)
`filename`	common_root.pdf or common_root.csv
`flip.palette`	logical; if TRUE it reverse the order of colors used for background (forest.plot)
`fnote`	vector of 5 footnotes. 5th row is traditionally reserved for filepath, table reference and time stamp. Populate from bottom up. (annotate.page)
`fnote.buffer`	fine-control of vertical position (annotate.page)
`foot.size`	default: 10; passed to grid.text via gp (annotate.page)
`fromthetop`	logical. If TRUE KM curve decends from 1, if FALSE KM curve ascends from 0 Ensure you have an appropriate censor.col passed above!
`gg.list`	a list of ggplot objects (sync.ylab.widths)
`head.size`	default: 10 (anotate.page)
`header.buffer`	fine-control of vertical position (anotate.page)
`interior`	a list of nrow*ncol grobs/ggplot objects to be displayed in the grid, ordered by row then col (build.page)
`interior.h`	a vector summing to 1 to indicate how to partition the heights (build.page)
`interior.w`	a vector summing to 1 to indicate how to partition the widths (build.page)
`killMissing`	logical used by bar.plot
`left.margin`	used by build.page and annotate.page; presumed to be inches
`linetype.col`	name of parent.df column associated with linetype
`line.size`	value gets passed to size within geom_line, geom_step
`linetype.palette`	values passed to scale_linetype_manual
`loadplan`	logical; if TRUE then it loads from the filename
`logd`	directory where log files are sent
`log.trans`	Logical; if TRUE log transformation is applied to x axis (ensure x.limits are positive!) (forest.plot)
`lower.lim`	column holding lower limit of CI
`main.theme`	text string name of theme to be called by theme_set,
`my.path`	path to main directory,
`ncol`	number of columns for the grid of graphics being built by build.page
`nrow`	number of rows for the grid of graphics being built by build.page
`nsubj.plot.label`	used in km.plot
`od`	directory where output files are sent
`outfile`	If (toPDF== TRUE & outfile == "") a .pdf file with root name taken from outputplan$outfile[which(outputplan$rcode ==source.code)]. Otherwise a .pdf will be created the value of outfile. The pdf is stored in mypath/od defined in setpaths.r.
`override`	override
`page.height`	used by build.page and annotate.page; presumed to be inches
`page.width`	used by build.page and annotate.page; presumed to be inches
`parent.df`	data.frame used by ggplot
`pdval`	value passed to position_dodge (lineplot)
`Point.Est`	point estimate
`pos`	used internally by some functions
`reportNR`	If TRUE, a plot with missing figure numbers and titles is produced
`response.col`	used by cdf.plottttt
`right.margin`	used by build.page and annotate.page; presumed to be inches
`shape.label`	value sets passed to labs
`shape.palette`	values passed to scale_shape_manual
`source.code`	This is intended to be a darapladib graphics driver file returning a graphic possibly with complete headers and footers.
`text.buffer`	used by bar.plot to control text placement
`test.dim`	logical. Assists with figure development. If TRUE it makes a call to grid.show.layout.
`text.col`	used by nsubj.plot
`text.col1`	name of column holding text for column 1 (table.plot)
`text.col2`	name of column holding text for column 2; can be NULL (table.plot)
`text.col3`	name of column holding text for column 3; can be NULL (table.plot)
`text.col4`	name of column holding text for column 4; can be NULL (table.plot)
`text.size`	value gets passed to geom_text
`title`	vector of title lines (annotate.page)
`title.buffer`	fine-control of vertical position (annotate.page)
`title.size`	default: 14; passed to grid.text via gp (annotate.page)
`toBMP`	Logical. If TRUE a .bmp file will be created. (run.specific)
`toEPS`	Logical. If TRUE a .eps file will be created. (run.specific)
`toJPEG`	Logical. If TRUE a .jpeg file will be created. (run.specific)
`top.axis.version`	ggplot object with intended top x-axis in bottom position (get.top.xaxis)
`top.margin`	used by build.page and annotate.page; presumed to be inches
`toPDF`	Logical. If TRUE a .pdf file will be created. If FALSE graphic is sent to screen. (run.specific)
`toPNG`	Logical. If TRUE a .png file will be created. (run.specific)
`toWMF`	Logical. If TRUE a .wmf file will be created. (run.specific)
`ulh`	vector for upper left headers (annotate.page)
`upper.lim`	column holding upper limit of CI (forest.plot)
`urh`	vector for upper right headers (annotate.page)
`UseSubset`	Corresponds to a column name in outputplan holding flags (all_in_one)
`x.col`	parent.df column associated with response vairable (line.plot, nsubj.plot)
`x.label`	value gets passed to labs
`x.limits`	value gets passed to scale_x_continuous
`x.ticks`	value gets passed to scale_x_continuous
`x.ticks.labels`	passed to scale_x_continuous
`y.col`	parent.df column associated with response vairable
`y.digits`	passed to scale_y_continuous label's, fmt (box.plot, line.plot)
`y.label`	value gets passed to labs
`y.label.col`	column holding labels for forest/dot/table plots
`y.label.rank.col`	column holding ranks for labels in forest/dot/table plots
`y.limits`	passed to scale_y_continuous
`y.rank.col`	column holding ranks for line items in forest/dot/table plots
`y.ticks`	passed to scale_y_continuous
`ymax.col`	name of parent.df column associated with ymax (line.plot errorbars)
`ymin.col`	name of parent.df column assoicated with ymin (line.plot errorbars)

Author(s)

Greg Cicconetti

This is a dataset structured for building figures using km.plot

Description

This is a dataset structured for building figures using km.plot

Author(s)

Greg Cicconetti

km.plot

Description

A function for creating harmonized Kaplan-Meier plots and accompanying At Risk table.

Usage

km.plot(
  parent.df,
  censor.col = "CENSOR",
  centime.col = "CENTIME.DAY",
  category.col = "REGION",
  category.palette = rainbow(5),
  at.risk.palette = rainbow(5),
  category.label = "Treatment Group",
  nsubj.plot.label = "Number at Risk",
  linetype.palette = 1:6,
  x.label = "Time Since Randomization",
  y.label = "Percetage of Subjects",
  x.limits = c(0, 48),
  x.ticks = seq(0, 48, 3),
  y.ticks = seq(0, 0.01, 0.005),
  y.limits = c(0, 0.01),
  line.size = 0.75,
  fromthetop = FALSE,
  text.size = 4
)
km.plot(
  parent.df,
  censor.col = "CENSOR",
  centime.col = "CENTIME.DAY",
  category.col = "REGION",
  category.palette = rainbow(5),
  at.risk.palette = rainbow(5),
  category.label = "Treatment Group",
  nsubj.plot.label = "Number at Risk",
  linetype.palette = 1:6,
  x.label = "Time Since Randomization",
  y.label = "Percetage of Subjects",
  x.limits = c(0, 48),
  x.ticks = seq(0, 48, 3),
  y.ticks = seq(0, 0.01, 0.005),
  y.limits = c(0, 0.01),
  line.size = 0.75,
  fromthetop = FALSE,
  text.size = 4
)

Arguments

`parent.df`	data.frame used by ggplot
`censor.col`	name of parent.df column associated with censor variable
`centime.col`	name of parent.df column associated with censored time
`category.col`	data.frame column associated with categorical variable (bar.plot, box.plot, cdf.plot, dot.plot, km.plot)
`category.palette`	colors assoicated with categorical variable
`at.risk.palette`	colors to be assocated with categorical variable in accompanying km.plot generated at.risk table
`category.label`	passed to x-axis label
`nsubj.plot.label`	used in km.plot
`linetype.palette`	values passed to scale_linetype_manual
`x.label`	value gets passed to labs
`y.label`	value gets passed to labs
`x.limits`	value gets passed to scale_x_continuous
`x.ticks`	value gets passed to scale_x_continuous
`y.ticks`	passed to scale_y_continuous
`y.limits`	passed to scale_y_continuous
`line.size`	value gets passed to size within geom_line, geom_step
`fromthetop`	logical. If TRUE KM curve decends from 1, if FALSE KM curve ascends from 0 Ensure you have an appropriate censor.col passed above!
`text.size`	value gets passed to geom_text

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

Examples

{
require(ggplot2); require(gridExtra)
data(km.data)
working.df <- km.data
head(working.df)
km.M <- km.plot(parent.df = subset(working.df, SEX== "M"),
      centime.col = "CENTIME.DAY",
      category.col = "TRTGRP",
      category.palette = c("red", "blue"),
      at.risk.palette = c("red","blue"),              
      linetype.palette = c("solid","dotted"), 
      y.limits=c(0,.01), 
      y.ticks=seq(0,.01,.005), 
      x.limits=c(-3,48),
      x.ticks=seq(0,48,6))
print(km.M[[1]])
print(km.M[[2]])
grid.arrange(km.M[[1]] + theme(legend.position= "bottom"), km.M[[2]], ncol=1)
comeback <- sync.ylab.widths(list(km.M[[1]]+ theme(legend.position= "bottom"), km.M[[2]]))
grid.arrange(comeback[[1]] , comeback[[2]], ncol=1)
build.page(interior.h = c(.8, .2),
      interior.w = c(1),
       ncol=1, nrow=2,
       interior = list(comeback[[1]], 
           comeback[[2]]))
}
{
require(ggplot2); require(gridExtra)
data(km.data)
working.df <- km.data
head(working.df)
km.M <- km.plot(parent.df = subset(working.df, SEX== "M"),
      centime.col = "CENTIME.DAY",
      category.col = "TRTGRP",
      category.palette = c("red", "blue"),
      at.risk.palette = c("red","blue"),              
      linetype.palette = c("solid","dotted"), 
      y.limits=c(0,.01), 
      y.ticks=seq(0,.01,.005), 
      x.limits=c(-3,48),
      x.ticks=seq(0,48,6))
print(km.M[[1]])
print(km.M[[2]])
grid.arrange(km.M[[1]] + theme(legend.position= "bottom"), km.M[[2]], ncol=1)
comeback <- sync.ylab.widths(list(km.M[[1]]+ theme(legend.position= "bottom"), km.M[[2]]))
grid.arrange(comeback[[1]] , comeback[[2]], ncol=1)
build.page(interior.h = c(.8, .2),
      interior.w = c(1),
       ncol=1, nrow=2,
       interior = list(comeback[[1]], 
           comeback[[2]]))
}

line.plot

Description

A function for creating harmonized line plots with optional errorbars.

Usage

line.plot(
  parent.df,
  category.palette = c("red", "blue"),
  linetype.palette = c("dotted", "blank", "solid", "blank"),
  line.size = 0.75,
  shape.palette = c(24, 21),
  x.label = "Visit",
  y.label = "Response",
  category.label = "Treatment Group",
  x.limits = NULL,
  x.ticks = NULL,
  x.ticks.labels = NULL,
  addBars = TRUE,
  bar.width = 1,
  pdval = 0.25,
  x.col = "XVALUES",
  y.col = "YVALUES",
  y.limits = NULL,
  y.ticks = NULL,
  category.color = "CATEGORY.COLOR",
  category.symbol.col = "CATEGORY.SYMBOL",
  y.digits = 0,
  ymin.col = "YMIN",
  ymax.col = "YMAX",
  linetype.col = "LTYPE"
)
line.plot(
  parent.df,
  category.palette = c("red", "blue"),
  linetype.palette = c("dotted", "blank", "solid", "blank"),
  line.size = 0.75,
  shape.palette = c(24, 21),
  x.label = "Visit",
  y.label = "Response",
  category.label = "Treatment Group",
  x.limits = NULL,
  x.ticks = NULL,
  x.ticks.labels = NULL,
  addBars = TRUE,
  bar.width = 1,
  pdval = 0.25,
  x.col = "XVALUES",
  y.col = "YVALUES",
  y.limits = NULL,
  y.ticks = NULL,
  category.color = "CATEGORY.COLOR",
  category.symbol.col = "CATEGORY.SYMBOL",
  y.digits = 0,
  ymin.col = "YMIN",
  ymax.col = "YMAX",
  linetype.col = "LTYPE"
)

Arguments

`parent.df`	data.frame used by ggplot
`category.palette`	colors assoicated with categorical variable
`linetype.palette`	values passed to scale_linetype_manual
`line.size`	value gets passed to size within geom_line, geom_step
`shape.palette`	values passed to scale_shape_manual
`x.label`	value gets passed to labs
`y.label`	value gets passed to labs
`category.label`	passed to x-axis label
`x.limits`	value gets passed to scale_x_continuous
`x.ticks`	value gets passed to scale_x_continuous
`x.ticks.labels`	passed to scale_x_continuous
`addBars`	logical to add error bars (line.plot)
`bar.width`	used by line.plot
`pdval`	value passed to position_dodge (lineplot)
`x.col`	parent.df column associated with response vairable (line.plot, nsubj.plot)
`y.col`	parent.df column associated with response vairable
`y.limits`	passed to scale_y_continuous
`y.ticks`	passed to scale_y_continuous
`category.color`	data.frame column assocated with aes color mapping (forest.plot, line.plot, nsubj.plot, table.plot)
`category.symbol.col`	used by line.plot
`y.digits`	passed to scale_y_continuous label's, fmt (box.plot, line.plot)
`ymin.col`	name of parent.df column assoicated with ymin (line.plot errorbars)
`ymax.col`	name of parent.df column associated with ymax (line.plot errorbars)
`linetype.col`	name of parent.df column associated with linetype

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti/David Wade

lineplot.data

Description

lineplot.data

Usage

data("lineplot.data")data("lineplot.data")

Format

A data frame with 190 observations on the following 17 variables.

Analysis.Visit..N.: a numeric vector
Analysis.Visit: a factor with levels BASELINE DAY 1 SCREEN WEEK -2 SCREEN WEEK -4 WEEK 10 WEEK 12 WEEK 14 WEEK 16 WEEK 18 WEEK 2 WEEK 20 WEEK 21 WEEK 22 WEEK 23 WEEK 24 WEEK 28 FOLLOW-UP WEEK 4 WEEK 6 WEEK 8
tt_segorder: a numeric vector
X.: a factor with levels Analysis Value
Order.of.Statistical.List: a numeric vector
X..1: a factor with levels 25th Percentile 75th Percentile LCLM Max. Mean Median Min. n SD UCLM
Summary.Level.Variable.Added.by.TU_STATSWITHTOTAL: a numeric vector
NAME.OF.FORMER.VARIABLE: a factor with levels TT_RESULT
LABEL.OF.FORMER.VARIABLE: a factor with levels Result - formatted
Not.Assigned..N.3.: a numeric vector
Control..N.10.: a numeric vector
X4.mg..N.11.: a numeric vector
X6.mg..N.16.: a numeric vector
X8.mg..N.8.: a numeric vector
X10.mg..N.11.: a numeric vector
X12.mg..N.6.: a numeric vector
X.N.1.: a numeric vector

Details

No details.

Examples

data(lineplot.data)
## maybe str(lineplot.data) ; plot(lineplot.data) ...
data(lineplot.data)
## maybe str(lineplot.data) ; plot(lineplot.data) ...

nsubj.plot

Description

A function to create tables to accompany KMs and lineplots

Usage

nsubj.plot(
  parent.df,
  category.palette = c("red", "blue"),
  x.label = "Number of Subjects",
  y.label = "Treatment\nGroup",
  text.size = 4,
  x.col = "XVALUES",
  text.col = "N",
  category.color = "CATEGORY",
  x.limits = c(0.5, 18),
  x.ticks = unique(parent.df$XVALUES),
  x.ticks.labels = unique(parent.df$XVALUES)
)
nsubj.plot(
  parent.df,
  category.palette = c("red", "blue"),
  x.label = "Number of Subjects",
  y.label = "Treatment\nGroup",
  text.size = 4,
  x.col = "XVALUES",
  text.col = "N",
  category.color = "CATEGORY",
  x.limits = c(0.5, 18),
  x.ticks = unique(parent.df$XVALUES),
  x.ticks.labels = unique(parent.df$XVALUES)
)

Arguments

`parent.df`	data.frame used by ggplot
`category.palette`	colors assoicated with categorical variable
`x.label`	value gets passed to labs
`y.label`	value gets passed to labs
`text.size`	value gets passed to geom_text
`x.col`	parent.df column associated with response vairable (line.plot, nsubj.plot)
`text.col`	used by nsubj.plot
`category.color`	data.frame column assocated with aes color mapping (forest.plot, line.plot, nsubj.plot, table.plot)
`x.limits`	value gets passed to scale_x_continuous
`x.ticks`	value gets passed to scale_x_continuous
`x.ticks.labels`	passed to scale_x_continuous

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti/David Wade

This is a dataset structured to facilitate mass figure production

Description

This is a dataset structured to facilitate mass figure production

Author(s)

Greg Cicconetti

This is a dataset that would need some pre-processing ahead of using line.plot

Description

This is a dataset that would need some pre-processing ahead of using line.plot

Author(s)

Greg Cicconetti

Refresh the Output Plan

Description

Reloads outputplan_study.csv file and applies canonical formatting changes.

Usage

refresh.outputplan(
  loadplan = TRUE,
  filename = "outputplan.csv",
  pos = 1,
  envir = as.environment(pos)
)
refresh.outputplan(
  loadplan = TRUE,
  filename = "outputplan.csv",
  pos = 1,
  envir = as.environment(pos)
)

Arguments

`loadplan`	logical; if TRUE then it loads from the filename
`filename`	common_root.pdf or common_root.csv
`pos`	used internally by some functions
`envir`	used internally by some functions

Details

Ensure all columns are read in as character vectors. Ensure all missing entries are replaced with blank character string. Ensure all escape characters for carrige returns are respected. Grabs the 'modified time' from file attributes associated with .csv files named in the outputplan.

Author(s)

Greg Cicconetti

run.specific

Description

This function sources a .r driver file and sends its product to a newly opened 8.5in x 11in screen or a pdf file with 8.5in x 11in dimensions.

Usage

run.specific(
  source.code = "g_AErr2.r",
  outfile = "",
  toPDF = FALSE,
  toWMF = FALSE,
  toJPEG = FALSE,
  toPNG = FALSE,
  toBMP = FALSE,
  toEPS = FALSE,
  dpires = 600,
  use.log = FALSE
)
run.specific(
  source.code = "g_AErr2.r",
  outfile = "",
  toPDF = FALSE,
  toWMF = FALSE,
  toJPEG = FALSE,
  toPNG = FALSE,
  toBMP = FALSE,
  toEPS = FALSE,
  dpires = 600,
  use.log = FALSE
)

Arguments

`source.code`	This is intended to be a darapladib graphics driver file returning a graphic possibly with complete headers and footers.
`outfile`	If (toPDF== TRUE & outfile == "") a .pdf file with root name taken from outputplan$outfile[which(outputplan$rcode ==source.code)]. Otherwise a .pdf will be created the value of outfile. The pdf is stored in mypath/od defined in setpaths.r.
`toPDF`	Logical. If TRUE a .pdf file will be created. If FALSE graphic is sent to screen. (run.specific)
`toWMF`	Logical. If TRUE a .wmf file will be created. (run.specific)
`toJPEG`	Logical. If TRUE a .jpeg file will be created. (run.specific)
`toPNG`	Logical. If TRUE a .png file will be created. (run.specific)
`toBMP`	Logical. If TRUE a .bmp file will be created. (run.specific)
`toEPS`	Logical. If TRUE a .eps file will be created. (run.specific)
`dpires`	passed to devices
`use.log`	logical to write a log file

Author(s)

David wade

start_session_log

Description

A function to start logging the session history for a graphic driver run

Usage

start_session_log(
  x,
  outputfile = "example.PDF",
  pos = 1,
  envir = as.environment(pos),
  ...
)
start_session_log(
  x,
  outputfile = "example.PDF",
  pos = 1,
  envir = as.environment(pos),
  ...
)

Arguments

`x`	used internally
`outputfile`	passed to name the session history log file
`pos`	used internally by some functions
`envir`	used internally by some functions
`...`	additional params

Details

Note that the stop_session_log function is used to stop the logging and save the log file.

Value

No objects are returned by this function.

Author(s)

David Wade

stop_session_log

Description

A function to stop logging the session history for a graphic driver run and save the session history file

Usage

stop_session_log()
stop_session_log()

Details

Note that the start_session_log function is used to start the logging, and it must be called first.

Value

No objects are returned by this function.

Author(s)

David Wade

This is a dataset that would need some pre-processing ahead of using line.plot

Description

This is a dataset that would need some pre-processing ahead of using line.plot

Author(s)

Greg Cicconetti

sync.ylab.widths

Description

Aligns the widths of ggplot objects to ensure common plot regions. The maximum length required for y-axis labels among the list is determined and applied to the other plots. This assists in syncing the widths of ggplot objects for the purpose of align figures on a page.

Usage

sync.ylab.widths(gg.list, default.length = 2)
sync.ylab.widths(gg.list, default.length = 2)

Arguments

`gg.list`	a list of ggplot objects (sync.ylab.widths)
`default.length`	set to 2

Author(s)

Greg Cicconetti

table.plot

Description

A function for creating harmonized table plots with A function for plotting columns of text in a figure offering compatiability with forest.plot and dot.plot.

Usage

table.plot(
  parent.df,
  y.rank.col = "Subcategory",
  category.color = "Treatment",
  text.col1 = "Point_Est",
  text.col2 = NULL,
  text.col3 = NULL,
  text.col4 = NULL,
  text.size = 12,
  xtick.labs = c("", "", ""),
  x.limits = NULL,
  y.limits = NULL,
  x.label = "Text",
  y.label = "Item",
  y.label.rank.col = "rank",
  y.label.col = "subcategory",
  category.palette = c("red", "blue")
)
table.plot(
  parent.df,
  y.rank.col = "Subcategory",
  category.color = "Treatment",
  text.col1 = "Point_Est",
  text.col2 = NULL,
  text.col3 = NULL,
  text.col4 = NULL,
  text.size = 12,
  xtick.labs = c("", "", ""),
  x.limits = NULL,
  y.limits = NULL,
  x.label = "Text",
  y.label = "Item",
  y.label.rank.col = "rank",
  y.label.col = "subcategory",
  category.palette = c("red", "blue")
)

Arguments

`parent.df`	data.frame used by ggplot
`y.rank.col`	column holding ranks for line items in forest/dot/table plots
`category.color`	data.frame column assocated with aes color mapping (forest.plot, line.plot, nsubj.plot, table.plot)
`text.col1`	name of column holding text for column 1 (table.plot)
`text.col2`	name of column holding text for column 2; can be NULL (table.plot)
`text.col3`	name of column holding text for column 3; can be NULL (table.plot)
`text.col4`	name of column holding text for column 4; can be NULL (table.plot)
`text.size`	value gets passed to geom_text
`xtick.labs`	xtick labels
`x.limits`	value gets passed to scale_x_continuous
`y.limits`	passed to scale_y_continuous
`x.label`	value gets passed to labs
`y.label`	value gets passed to labs
`y.label.rank.col`	column holding ranks for labels in forest/dot/table plots
`y.label.col`	column holding labels for forest/dot/table plots
`category.palette`	colors assoicated with categorical variable

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

figuRes2 themes

Description

Adapts theme_grey() found in ggplot2

Usage

theme_grey2_nomargins(base_size = 12, base_family = "")

theme_grey2_default_margins(base_size = 12, base_family = "")

theme_bw2_nomargins(base_size = 12, base_family = "")

theme_bw2_default_margins(base_size = 12, base_family = "")

theme_table_nomargins(base_size = 12, base_family = "")
theme_grey2_nomargins(base_size = 12, base_family = "")

theme_grey2_default_margins(base_size = 12, base_family = "")

theme_bw2_nomargins(base_size = 12, base_family = "")

theme_bw2_default_margins(base_size = 12, base_family = "")

theme_table_nomargins(base_size = 12, base_family = "")

Arguments

`base_size`	used in set_theme calls
`base_family`	used in set_theme calls

Details

axis.text colour changed from "grey50" to "black"; legend.position changed from "right" to "bottom"; legend.direction changed to "horizontal"; plot.margin changed from default unit(c(1, 1, 0.5, 0.5), "lines") to unit(c(0, 0, 0, 0), "in")

Value

The returns a function that can be passed to ggplot2::theme_set

Functions

theme_grey2_default_margins(): Same as theme_grey2_nomargins but with margins set to ggplot defaults, unit(c(1, 1, 0.5, 0.5), "lines")
theme_bw2_nomargins(): Similar to theme_grey2
theme_bw2_default_margins(): Similar to theme_bw_nomargins but with margins set to ggplot defaults, unit(c(1, 1, 0.5, 0.5), "lines")
theme_table_nomargins(): alteration to theme_grey

Author(s)

Greg Cicconetti

Examples

{
ggplot2::theme_set(theme_grey2_nomargins())
}
{
ggplot2::theme_set(theme_grey2_nomargins())
}

Package 'figuRes2'

Help Index

all_in_one

Description

Usage

Arguments

Details

Value

Author(s)

annotate.page

Description

Usage

Arguments

Value

Author(s)

bar.plot

Description

Usage

Arguments

Value

Author(s)

Examples

This is a dataset structured for building figures using forest.plot

Description

Author(s)

box.plot

Description

Usage

Arguments

Value

Author(s)

Examples

This holds lines to a driver file created by the large-scale vignette

Description

Author(s)

build.page

Description

Usage

Arguments

Value

Author(s)

Examples

This is a dataset that would need some pre-processing ahead of using line.plot

Description

Author(s)

This is a dataset structured for building figures using cdf.plot

Description

Author(s)

cdf.plot

Description

Usage

Arguments

Value

Author(s)

Examples

check.ggplot.outliers

Description

Usage

Arguments

Details

Author(s)

default.settings

Description

Usage

Arguments

Details

Value

Author(s)

This is a dataset structured for building figures using bar.plot, box.plot, and cdf.plot

Description

Author(s)

dot.plot

Description

Usage

Arguments

Value

Author(s)

This holds lines to a driver file created by the large-scale vignette

Description

Author(s)