R/data.R

In cavei/MOSClip: Multi Omics Survival Clip

## Colors
MOSpalette <- c ("#E33402", "#04B880", "#3871CC", "#E5C002", "#8C04B6", "#01B7BF")
names(MOSpalette) <- c("red","green","blue","yellow","violet","teal")

MOSpaletteSchema <- data.frame(
  dark=grDevices::adjustcolor(MOSpalette,offset = c(-0.4, -0.4, -0.4, 0)),
  smart=MOSpalette,
  light=grDevices::adjustcolor(MOSpalette,offset = c(0.5, 0.5, 0.5, 0)),
  transparent=grDevices::adjustcolor(MOSpalette, alpha.f = 0.6),
  white=grDevices::adjustcolor(MOSpalette,offset = c(0.96, 0.96, 0.96, 0)),
  stringsAsFactors = FALSE, check.names = FALSE)
rownames(MOSpaletteSchema) <- c("red","green","blue","yellow","violet","teal")

# The followings are functions, use it like redShades(100) where 100 is the number of shades.
# In the case of binary map we can use redShades(2).
redShades <- grDevices::colorRampPalette(
  colors=c(MOSpaletteSchema["red","white"],
           MOSpaletteSchema["red","smart"]),
  bias=1, space="rgb",
  interpolate="linear", alpha=FALSE)

greenShades <- grDevices::colorRampPalette(
  colors=c(MOSpaletteSchema["green","white"],
           MOSpaletteSchema["green","smart"]),
  bias=1, space="rgb",
  interpolate="linear", alpha=FALSE)

blueShades <- grDevices::colorRampPalette(
  colors=c(MOSpaletteSchema["blue","white"],
           MOSpaletteSchema["blue","smart"]),
  bias=1, space="rgb",
  interpolate="linear", alpha=FALSE)

yellowShades <- grDevices::colorRampPalette(
  colors=c(MOSpaletteSchema["yellow","white"],
           MOSpaletteSchema["yellow","smart"]),
  bias=1, space="rgb",
  interpolate="linear", alpha=FALSE)

violetShades <- grDevices::colorRampPalette(
  colors=c(MOSpaletteSchema["violet","white"],
           MOSpaletteSchema["violet","smart"]),
  bias=1, space="rgb",
  interpolate="linear", alpha=FALSE)

tealShades <- grDevices::colorRampPalette(
  colors=c(MOSpaletteSchema["teal","white"],
           MOSpaletteSchema["teal","smart"]),
  bias=1, space="rgb",
  interpolate="linear", alpha=FALSE)

pvalueShades <- grDevices::colorRampPalette(
  colors=c("#edf7f5", "#2796bd"),
  bias=20, space="rgb",
  interpolate="linear", alpha=FALSE)(100)

omicsRegexp <- "(PC[0-9]+|[1-9]k[1-9]?|TRUE|FALSE|POS|NEG|POSTRUE|NEGTRUE)$"