graphic.params {figuRes2}

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
)

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 associated with ymin (line.plot errorbars)

Value

This function is just a convenient location to store argument names.

Author(s)

Greg Cicconetti