qpToolkit: qPharmetra R Tools

# ROXYGEN Documentation
#' qPharmetra Colors
#' @description a set of qPharmetra colors to be used for plotting
#' @section Notes:
#' Colors are named rgb codes
#' @return qPharmetra logo colors qp.blue,qp.green, and the following low saturated colors: lime,apple,emerald, cobalt, cyan, cobalt, indigo, violet, pink, magenta, crimson, ketchup, orange,amber,yellow,brown,olive,steel,mauve,taupe.
#' @export qp.colors qp.green qp.blue qp.colors qp.colors.sorted lime apple emerald cobalt cyan cobalt indigo violet pink magenta crimson ketchup orange amber yellow brown olive steel mauve taupe gray blue green red purple teal obs.color loi.color smooth.color smooth.ci.color lin.fit.col abline.color box.plot.color histogram.color abline.color.box ipred.color pred.color PI.ci.med.arcol PI.real.med.col PI.real.down.col PI.real.up.col PI.ci.down.arcol PI.ci.up.arcol pred.lty ipred.lty
#' @family qpcolors
#' @examples
#' ## the greens and the blues
#' par(mfrow = c(1,1), pty = 's')
#' nc = length(blue)
#' cols = c(8,8,8,8,8,4,2,1,1,1)

#' plot(1:nc, seq(-0.45,0.3,length=nc), type = 'n', axes = FALSE, xlab ="", ylab = "",
#'  xlim = c(0.5, nc + 0.5))
#' for(i in 1:nc)
#' {
#'   polygon(c(i-0.45, i+0.45, i+0.45, i-0.45), c(0.16, 0.16, 0.29, 0.29),
#'           col = green[i], angle = -1, density = -1, border=0)
#'   text(i,0.225,paste("green[",i,"]", sep = ""), cex = 0.6, col = green[cols][i])
#'   polygon(c(i-0.45, i+0.45, i+0.45, i-0.45), c(0.01, 0.01, 0.14, 0.14),
#'           col = blue[i], angle = -1, density = -1, border=0)
#'   text(i,0.075,paste("blue[",i,"]", sep = ""), cex = 0.6, col = blue[cols][i])
#'   polygon(c(i-0.45, i+0.45, i+0.45, i-0.45), c(-0.01, -0.01, -0.14, -0.14),
#'           col = red[i], angle = -1, density = -1, border=0)
#'   text(i,-0.075,paste("red[",i,"]", sep = ""), cex = 0.6, col = red[cols][i])
#'   polygon(c(i-0.45, i+0.45, i+0.45, i-0.45), c(-0.16, -0.16, -0.29, -0.29),
#'           col = purple[i], angle = -1, density = -1, border=0)
#'   text(i,-0.225,paste("purple[",i,"]", sep = ""), cex = 0.6, col = purple[cols][i])
#'   polygon(c(i-0.45, i+0.45, i+0.45, i-0.45), c(-0.31, -0.31, -0.44, -0.44),
#'           col = gray[i], angle = -1, density = -1, border=0)
#'   text(i,-0.375,paste("gray[",i,"]", sep = ""), cex = 0.6, col = gray[cols][i])
#' }
#' 
#' library(lattice)
#' lapply(list(qp.colors,qp.colors.sorted), function(my.colors)
#' xyplot(yval ~ xval | color
#'       , data = expand.grid(xval = 1, yval = 1, color = names(my.colors))
#'       , xlim = c(0,1)
#'       , ylim = c(0,1)
#'       , as.table = TRUE
#'       , panel = function(x,y,...)
#'       {
#'         panel.rect(xleft = 0, ybottom = 0
#'                    , xright = 1, ytop = 1
#'                    , col = my.colors[panel.number()]
#'         )
#'         ltext(x = 0.5, y = 0.5
#'               , my.colors[panel.number()], col = rgb(0.99,0.99,0.99)
#'               , cex = 0.75
#'         )
#'       }
#'       , aspect = 1
#'       , par.strip.text = list(cex = 1)
#'       , scales = list(y = list(at = NULL), x = list(at = NULL))
#'       , ylab = ""
#'       , xlab = ""
#'    )
#' )
#'
#' par(pty = "m")
#' plot(0:1,0:1, type = 'n',axes = FALSE, xlab = "", ylab = "")
#' polygon(x = c(0,1,1,0),y=c(0.5,0.5,0,0), col = qp.blue, border = FALSE)
#' polygon(x = c(0,1,1,0),y=c(1,1,0.5,0.5), col = qp.green, border = FALSE)
#' text(0.5,0.75, "qPharmetra", col = "white", cex = 5)
#' text(0.5,0.25, "qPharmetra", col = "white", cex = 5)
#' 

qp.blue = rgb(20/255,74/255,144/255)
qp.green = rgb(76/255,181/255,79/255)

nc = 7
blue  	= rgb(seq(230,0,length=nc),seq(230,0,length=nc),seq(255,240,length=nc),maxColorValue = 255) 
green		= rgb(seq(230,0,length=nc),seq(255,150,length=nc), seq(230,0,length=nc), maxColorValue = 255)
red		= rgb(seq(255,240,length=nc),seq(230,10,length=nc), seq(230,10,length=nc), maxColorValue = 255)
purple	= rgb(seq(255,240,length=nc),seq(230,10,length=nc), seq(255,240,length=nc), maxColorValue = 255)
gray        = rgb(seq(242,0,length=10),seq(242,0,length=10),seq(242,0,length=10), maxColorValue = 255)

## add superdark example as eighth option
blue  = c(blue , rgb(0,0,150,maxColorValue = 255),rgb(0,0,80,maxColorValue = 255), rgb(0,0,30,maxColorValue = 255))
green = c(green, rgb(0,150,0,maxColorValue = 255),rgb(0,80,0,maxColorValue = 255),rgb(0,30,0,maxColorValue = 255))
red   = c(red  , rgb(150,0,0,maxColorValue = 255),rgb(80,0,0,maxColorValue = 255),rgb(30,0,0,maxColorValue = 255))
purple= c(purple, rgb(150,0,150,maxColorValue = 255),rgb(80,0,80,maxColorValue = 255),rgb(30,0,30,maxColorValue = 255))

nc = length(blue)
names(blue) = paste("blue", 1:nc,sep = "")
names(green) = paste("green", 1:nc,sep = "")
names(red) = paste("red", 1:nc,sep = "")
names(purple) = paste("purple", 1:nc,sep = "")
names(gray) = paste("gray", 1:nc,sep = "")


lime =  rgb(164/255,196/255,0/255)
apple = rgb(96/255,169/255,23/255)
emerald = rgb(0,138/255,0)
teal = rgb(0,171/255,169/255)
cyan = rgb(27/255,161/255,226/255)
cobalt = rgb(0,80/255,239/255)
indigo = rgb(106/255,0,1)
violet = rgb(170/255,0,1)
pink = rgb(244/255,114/255,208/255)
magenta = rgb(216/255,0,115/255)
crimson = rgb(162/255,0,37/255)
ketchup = rgb(229/255,20/255,0)
orange = rgb(250/255,104/255,0)
amber = rgb(240/255,163/255,10/255)
yellow = rgb(227/255,200/255,0)
brown = rgb(130/255,90/255,44/255)
olive = rgb(109/255,135/255,100/255)
steel = rgb(100/255,118/255,135/255)
mauve = rgb(118/255,96/255,138/255)
taupe = rgb(135/255,121/255,78/255)


qp.colors = c(qp.blue = qp.blue,
              qp.green = qp.green, 
              ketchup = ketchup, 
              amber = amber, 
              brown = brown, 
              cobalt = cobalt,
              emerald = emerald, 
              orange = orange, 
              indigo = indigo, 
              apple = apple, 
              cyan = cyan, 
              violet = violet, 
              pink = pink, 
              steel = steel, 
              crimson = crimson, 
              yellow = yellow, 
              teal = teal,
              olive = olive, 
              lime = lime, 
              magenta = magenta, 
              mauve = mauve, 
              taupe = taupe
)

qp.colors.sorted =  c(
   lime = lime, 
   apple = apple, 
   qp.green = qp.green,
   emerald = emerald,
   teal = teal,
   cyan = cyan, 
   cobalt = cobalt,
   qp.blue = qp.blue,
   indigo = indigo, 
   violet = violet,
   pink = pink,
   magenta = magenta,
   ketchup = ketchup, 
   crimson = crimson,
   brown = brown,
   orange = orange,
   amber = amber, 
   yellow = yellow, 
   olive = olive, 
   taupe = taupe, 
   mauve = mauve, 
   steel = steel
)

## autographs colors

obs.color="slategrey"
loi.color="black" 
smooth.color=emerald
smooth.ci.color=emerald 
lin.fit.col="blue"
abline.color="darkslategrey"
box.plot.color="#2C858D"
histogram.color="#2C858D"
abline.color.box="#6A2D8A"
pred.color=ketchup
#ipred.lty = 1
ipred.color=cobalt 
#pred.lty = 1
PI.ci.med.arcol = emerald
PI.real.med.col= "blue"
PI.real.down.col="darkslategrey"
PI.real.up.col="darkslategrey"
PI.ci.down.arcol = gray(0.2)
PI.ci.up.arcol = gray(0.2)

nms <- ls()

use_data(
   qp.blue,
   qp.green,
   blue,
   green,
   red,
   purple,
   gray,
   blue,
   green,
   red,
   purple,
   lime,
   apple,
   emerald,
   teal,
   cyan,
   cobalt,
   indigo,
   violet,
   pink,
   magenta,
   crimson,
   ketchup,
   orange,
   amber,
   yellow,
   brown,
   olive,
   steel,
   mauve,
   taupe,
   qp.colors,
   qp.colors.sorted,
   obs.color,
   loi.color,
   smooth.color,
   smooth.ci.color,
   lin.fit.col,
   abline.color,
   box.plot.color,
   histogram.color,
   abline.color.box,
   pred.color,
   ipred.color,
   PI.ci.med.arcol,
   PI.real.med.col,
   PI.real.down.col,
   PI.real.up.col,
   PI.ci.down.arcol,
   PI.ci.up.arcol
)