scale filled color to customized giemsa color.

Description

scale filled color to customized giemsa color.

Usage

scale_fill_giemsa(fill = getOption("biovizBase")$cytobandColor)

Arguments

Value

a list.

Author(s)

Tengfei Yin

Examples

getOption("biovizBase")$cytobandColor
library(biovizBase)
data(hg19IdeogramCyto)
p1 <- autoplot(hg19IdeogramCyto, layout = "karyogram", aes(fill  =
gieStain))
p1
p1 + scale_fill_giemsa()

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ggbio)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ggbio/scale_fill_giemsa.Rd_%03d_medium.png", width=480, height=480)
> ### Name: scale_fill_giemsa
> ### Title: scale filled color to customized giemsa color.
> ### Aliases: scale_fill_giemsa
> 
> ### ** Examples
> 
> getOption("biovizBase")$cytobandColor
     gneg     stalk      acen      gpos      gvar     gpos1     gpos2     gpos3 
"grey100"  "brown3"  "brown4"   "grey0"   "grey0" "#FFFFFF" "#FCFCFC" "#F9F9F9" 
    gpos4     gpos5     gpos6     gpos7     gpos8     gpos9    gpos10    gpos11 
"#F7F7F7" "#F4F4F4" "#F2F2F2" "#EFEFEF" "#ECECEC" "#EAEAEA" "#E7E7E7" "#E5E5E5" 
   gpos12    gpos13    gpos14    gpos15    gpos16    gpos17    gpos18    gpos19 
"#E2E2E2" "#E0E0E0" "#DDDDDD" "#DADADA" "#D8D8D8" "#D5D5D5" "#D3D3D3" "#D0D0D0" 
   gpos20    gpos21    gpos22    gpos23    gpos24    gpos25    gpos26    gpos27 
"#CECECE" "#CBCBCB" "#C8C8C8" "#C6C6C6" "#C3C3C3" "#C1C1C1" "#BEBEBE" "#BCBCBC" 
   gpos28    gpos29    gpos30    gpos31    gpos32    gpos33    gpos34    gpos35 
"#B9B9B9" "#B6B6B6" "#B4B4B4" "#B1B1B1" "#AFAFAF" "#ACACAC" "#AAAAAA" "#A7A7A7" 
   gpos36    gpos37    gpos38    gpos39    gpos40    gpos41    gpos42    gpos43 
"#A4A4A4" "#A2A2A2" "#9F9F9F" "#9D9D9D" "#9A9A9A" "#979797" "#959595" "#929292" 
   gpos44    gpos45    gpos46    gpos47    gpos48    gpos49    gpos50    gpos51 
"#909090" "#8D8D8D" "#8B8B8B" "#888888" "#858585" "#838383" "#808080" "#7E7E7E" 
   gpos52    gpos53    gpos54    gpos55    gpos56    gpos57    gpos58    gpos59 
"#7B7B7B" "#797979" "#767676" "#737373" "#717171" "#6E6E6E" "#6C6C6C" "#696969" 
   gpos60    gpos61    gpos62    gpos63    gpos64    gpos65    gpos66    gpos67 
"#676767" "#646464" "#616161" "#5F5F5F" "#5C5C5C" "#5A5A5A" "#575757" "#545454" 
   gpos68    gpos69    gpos70    gpos71    gpos72    gpos73    gpos74    gpos75 
"#525252" "#4F4F4F" "#4D4D4D" "#4A4A4A" "#484848" "#454545" "#424242" "#404040" 
   gpos76    gpos77    gpos78    gpos79    gpos80    gpos81    gpos82    gpos83 
"#3D3D3D" "#3B3B3B" "#383838" "#363636" "#333333" "#303030" "#2E2E2E" "#2B2B2B" 
   gpos84    gpos85    gpos86    gpos87    gpos88    gpos89    gpos90    gpos91 
"#292929" "#262626" "#242424" "#212121" "#1E1E1E" "#1C1C1C" "#191919" "#171717" 
   gpos92    gpos93    gpos94    gpos95    gpos96    gpos97    gpos98    gpos99 
"#141414" "#121212" "#0F0F0F" "#0C0C0C" "#0A0A0A" "#070707" "#050505" "#020202" 
  gpos100 
"#000000" 
> library(biovizBase)
> data(hg19IdeogramCyto)
> p1 <- autoplot(hg19IdeogramCyto, layout = "karyogram", aes(fill  =
+ gieStain))
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning messages:
1: In getIdeoGR(data) :
  geom(ideogram) need valid seqlengths information for accurate mapping,
                 now use reduced information as ideogram... 
2: In getIdeoGR(data) :
  geom(ideogram) need valid seqlengths information for accurate mapping,
                 now use reduced information as ideogram... 
> p1
> p1 + scale_fill_giemsa()
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>