title	author	date	output	vignette
ggr intro	JF Rami	2016-11-30	rmarkdown::html_vignette	%\VignetteIndexEntry{Vignette Title} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

library(ggr)
library(knitr)

Let's read two example files provided with the package

mymap<-read.table(system.file("extdata","Nguepjop.et.al.2016.map.txt",package="ggr"))
myg<-read.table(system.file("extdata","Nguepjop.et.al.2016.txt",package="ggr"))

The files look like that:

V1	V2	V3
Ai124H2_A1	A04	0.0
Seq12E10_A	A04	16.4
Seq3B10_A	A04	30.8
gi-0832_A	A04	32.0
Ah3TC39B04_A	A04	32.0
Ad92K17_A	A04	32.0

V1	V2	V3	V4	V5	V6	V7	V8	V9	V10	V11	V12	V13	V14	V15	V16	V17	V18	V19	V20	V21	V22	V23	V24	V25	V26	V27	V28	V29	V30	V31	V32	V33	V34	V35	V36	V37	V38	V39	V40	V41	V42	V43	V44	V45	V46	V47	V48	V49	V50	V51	V52	V53	V54	V55	V56	V57	V58	V59	V60	V61	V62	V63	V64	V65	V66	V67	V68	V69	V70	V71	V72	V73	V74	V75	V76	V77	V78	V79	V80	V81	V82	V83	V84	V85	V86	V87	V88	V89	V90	V91
Ai124H2_A1	B	H	H	H	H	A	-	H	H	H	H	B	H	H	B	H	A	H	-	H	H	B	H	H	H	H	A	H	B	B	B	A	B	H	B	B	B	-	H	H	H	A	H	B	H	H	H	H	H	A	H	A	H	B	A	A	A	H	H	H	B	B	-	B	A	A	H	H	H	H	H	H	B	H	H	H	H	H	H	H	H	H	B	H	H	H	A	H	H	B
Seq12E10_A	B	A	H	H	A	A	-	H	H	A	H	B	H	H	B	H	A	H	-	H	H	B	H	H	H	H	A	A	B	B	B	A	B	A	H	A	B	-	H	H	A	A	H	H	H	H	A	-	A	B	H	A	H	B	A	A	A	H	H	H	B	B	-	B	A	A	H	A	H	H	-	H	A	H	H	H	A	H	H	A	H	A	B	A	A	H	B	H	H	B
Seq3B10_A	B	A	H	H	A	A	-	H	A	A	H	H	H	B	B	H	A	H	-	A	H	B	H	A	H	B	A	B	B	B	A	A	B	A	H	B	B	-	H	H	A	A	H	H	H	H	A	-	A	A	H	H	H	B	A	A	A	H	A	A	B	B	-	B	A	A	H	A	H	B	-	H	A	H	A	H	A	H	H	A	H	A	B	A	A	H	A	A	H	B
gi-0832_A	B	A	H	H	A	A	-	H	H	A	H	H	H	B	B	H	A	A	-	A	H	B	H	A	H	B	A	B	B	B	A	A	B	A	H	B	B	-	H	H	A	A	H	H	H	H	A	-	A	A	H	H	H	B	A	A	A	H	A	A	B	B	-	B	A	A	H	A	H	B	-	H	A	H	A	H	A	H	H	A	H	A	B	A	A	H	A	A	H	B
Ah3TC39B04_A	B	A	H	H	A	A	-	H	H	A	H	H	H	B	B	H	A	A	-	A	H	B	H	A	H	B	A	B	B	B	A	A	B	A	H	B	B	-	H	H	A	A	H	H	H	H	A	-	A	A	H	H	H	B	A	A	A	H	A	A	B	B	-	B	A	A	H	A	H	B	-	H	A	H	A	H	A	H	H	A	H	A	B	A	A	H	A	A	H	B
Ad92K17_A	B	A	H	H	A	A	-	H	H	A	H	H	H	B	B	H	A	A	-	A	H	B	H	A	H	B	A	B	B	B	A	A	B	A	H	B	B	-	H	H	A	A	H	H	H	H	A	-	A	A	H	H	H	B	A	A	A	H	A	A	B	B	-	B	A	A	H	A	H	B	-	H	A	H	A	H	A	H	H	A	H	A	B	A	A	H	A	A	H	B

The map needs to be converted to the R/qtl format

mymap<-as.map(mymap)
mymap

## $A04
##   Ai124H2_A1   Seq12E10_A    Seq3B10_A    gi-0832_A Ah3TC39B04_A 
##          0.0         16.4         30.8         32.0         32.0 
##    Ad92K17_A   IPAHM395_A      PM120_A   IPAHM108_A   IPAHM105_A 
##         32.0         33.8         53.2         53.8         55.0 
##   Seq18C05_A     Ah-569_A Ah3TC13G05_A 
##         64.8         75.5         95.4 
## 
## $B04
## Ah3TC21A09_B    Seq2D01_B    Seq3B06_B Ah3TC39B04_B    Seq3B10_B 
##          0.0          0.0          7.9         12.5         14.2 
##    TC11C06_B  IPAHM105_B1   IPAHM108_B     RN9C02_B     TC1H04_B 
##         23.4         26.8         27.9         29.6         33.6 
##  Seq15C12_B1     Ah-569_B    RN12E01_B Ah3TC13G05_B 
##         35.3         41.1         50.6         65.9

Let's get the genotype codes that are used in the genotype table myg :

codes<-unique(c(as.matrix(myg[,-1])))
codes

## [1] "B" "H" "A" "-"

We will need a vector of named colors, using codes as names, to plot the genotypes blocs

mycolors<-c("green","yellow","red","white")
names(mycolors)<-codes
mycolors

##        B        H        A        - 
##  "green" "yellow"    "red"  "white"

Let's use the gg function with myg, mymap and mycolors. There is a couple of parameters to explore, especially parameters of the maplot function that is used to plot the map.

gg(x = myg,map = mymap,col =mycolors,lmarg = 0.06 ,inter=0.1,sw=-1,first = 0.05,position=F)