diff --git a/article/.RData b/article/.RData index 63e30f646e8bdfa1d421643ee217b8e35c8a868e..be74b65cb8337cff9eae74d9df657d828ad50985 100644 Binary files a/article/.RData and b/article/.RData differ diff --git a/article/article_figures.Rmd b/article/article_figures.Rmd index e965f8a278288ed506c3cf020bc942c22ce76bc4..43c3bddf1e263c23eeaa8b207d9ac28b5d2d3fe9 100644 --- a/article/article_figures.Rmd +++ b/article/article_figures.Rmd @@ -283,25 +283,21 @@ colnames(peak1_tab) <- c("marker","chr","pos","allele\n1","allele\n2", "n\nHM1","n\nHM2","n\nHT","n\nNA") colnames(peak3_tab) <- c("marker","chr","pos","allele\n1","allele\n2", "n\nHM1","n\nHM2","n\nHT","n\nNA") -colnames(peak5_tab) <- c("marker","chr","pos","allele\n1","allele\n2", - "n\nHM1","n\nHM2","n\nHT","n\nNA") narrow_grid <- ggdraw() + - draw_plot(pheno_before_annot_data2,0,.75,.5,.25) + - draw_plot(pheno_before_annot_data3,.5,.75,.5,.25) + - draw_plot(peak1,0,.5,.3,.25) + - draw_plot(tableGrob(peak1_tab,rows=NULL),.3,.5,.7,.25) + - draw_plot(peak3,0,.25,.3,.25) + - draw_plot(tableGrob(peak3_tab,rows=NULL),.3,.25,.7,.25) + - draw_plot(peak5,0,0,.3,.25) + - draw_plot(tableGrob(peak5_tab,rows=NULL),.3,0,.7,.25) + - draw_plot_label(c("A","B","C","D","E","F","G","H"), - c(0,.5,0,.3,0,.3,.5,.7),c(1,1,.75,.75,.5,.5,.25,.25)) + draw_plot(pheno_before_annot_data2,0,.7,.5,.3) + + draw_plot(pheno_before_annot_data3,.5,.7,.5,.3) + + draw_plot(peak1,0,.35,.3,.3) + + draw_plot(tableGrob(peak1_tab,rows=NULL),.3,.35,.7,.3) + + draw_plot(peak3,0,0,.3,.3) + + draw_plot(tableGrob(peak3_tab,rows=NULL),.3,0,.7,.3) + + draw_plot_label(c("A","B","C","D","E","F"), + c(0,.5,0,.3,0,.3),c(1,1,.65,.65,.3,.3)) narrow_grid -ggsave(narrow_grid,file="figures/figS3prev.pdf",width=10,height=17) -ggsave(narrow_grid,file="figures/figS3prev.png",width=10,height=17) +ggsave(narrow_grid,file="figures/figS3prev.pdf",width=10,height=14) +ggsave(narrow_grid,file="figures/figS3prev.png",width=10,height=14) rm(peak1,peak1_tab,peak2,peak2_tab,peak3,peak3_tab,peak5,peak5_tab) ``` @@ -336,22 +332,18 @@ ggsave("figures/figS5.pdf",grid_scans,width=14,height = 5) ## Comparision of non mendelian/wrong alleles markers between the 4 datasets -```{r} -load("data2/tab2_data2.rda") -load("data3/tab2_data3.rda") -load("data4/tab2_data4.rda") +A REFAIRE!!!! +```{r} colnames(tab2_data2) <- c(colnames(tab2_data2)[1:3],paste0(colnames(tab2_data2)[4:ncol(tab2_data2)],".2")) colnames(tab2_data3) <- c(colnames(tab2_data3)[1:3],paste0(colnames(tab2_data3)[4:ncol(tab2_data3)],".3")) -colnames(tab2_data4) <- c(colnames(tab2_data4)[1:3],paste0(colnames(tab2_data4)[4:ncol(tab2_data4)],".4")) -tab_alldata <- full_join(tab2,tab2_data2) %>% full_join(.,tab2_data3) %>% full_join(.,tab2_data4) +tab_alldata <- full_join(tab2,tab2_data2) %>% full_join(.,tab2_data3) #keep all markers with non mendelian prop in at least 1 dataset -prop_rem <- tab_alldata %>% filter((exclude_poly==0&exclude_prop==1) | - (exclude_poly.2==0&exclude_prop.2==1) | - (exclude_poly.3==0&exclude_prop.3==1) | - (exclude_poly.4==0&exclude_prop.4==1)) +prop_rem <- tab_alldata %>% filter((exclude_poly==0&exclude_prop==1) | (exclude_poly==0&exclude_allele==1) | + (exclude_poly.2==0&exclude_prop.2==1) | (exclude_poly.2==0&exclude_allele.2==1) | + (exclude_poly.3==0&exclude_prop.3==1) | (exclude_poly.3==0&exclude_allele.3==1)) nrow(prop_rem) @@ -359,25 +351,24 @@ nrow(prop_rem) prop_rem %<>% mutate(exclpr_data1=case_when(exclude_poly==0&exclude_prop==1 ~ 1, T ~ 0)) %>% mutate(exclpr_data2=case_when(exclude_poly.2==0&exclude_prop.2==1 ~ 1, T ~ 0)) %>% mutate(exclpr_data3=case_when(exclude_poly.3==0&exclude_prop.3==1 ~ 1, T ~ 0)) %>% - mutate(exclpr_data4=case_when(exclude_poly.4==0&exclude_prop.4==1 ~ 1, T ~ 0)) %>% - mutate(sompr=exclpr_data1+exclpr_data2+exclpr_data3+exclpr_data4) + mutate(sompr=exclpr_data1+exclpr_data2+exclpr_data3) #note if marker retained in a data set prop_rem %<>% mutate(excl_data1=case_when((exclude_match+exclude_poly+exclude_na+exclude_prop+exclude_allele+exclude_estmap)==0 ~ 0, T ~ 1)) %>% mutate(excl_data2=case_when((exclude_match.2+exclude_poly.2+exclude_na.2+exclude_prop.2+exclude_allele.2+exclude_estmap.2)==0 ~ 0, T ~ 1)) %>% mutate(excl_data3=case_when((exclude_match.3+exclude_poly.3+exclude_na.3+exclude_prop.3+exclude_allele.3+exclude_estmap.3)==0 ~ 0, T ~ 1)) %>% - mutate(excl_data4=case_when((exclude_match.4+exclude_poly.4+exclude_na.4+exclude_prop.4+exclude_allele.4+exclude_estmap.4)==0 ~ 0, T ~ 1)) %>% - mutate(som=excl_data1+excl_data2+excl_data3+excl_data4) + mutate(som=excl_data1+excl_data2+excl_data3) #number of markers ok in a least 1 dataset -prop_rem %>% filter(som<4) %>% nrow() +prop_rem %>% filter(som<3) %>% nrow() #number of markers always removed -prop_rem %<>% mutate(notpoly=case_when(som==4 & (exclude_poly+exclude_poly.2+exclude_poly.3+exclude_poly.4==3) ~ 0, - som==4 & is.na(exclude_poly.2)==TRUE & (exclude_poly+exclude_poly.3+exclude_poly.4==2) ~ 0, - som==4 & (exclude_poly+exclude_poly.2+exclude_poly.3+exclude_poly.4==0) ~ 2, - som==4 & (exclude_poly+exclude_poly.2+exclude_poly.3+exclude_poly.4<3) & (exclude_poly+exclude_poly.2+exclude_poly.3+exclude_poly.4>0) ~ 1, - som==4 & is.na(exclude_poly.2)==TRUE & (exclude_poly+exclude_poly.3+exclude_poly.4<2) & (exclude_poly+exclude_poly.3+exclude_poly.4>0) ~ 1)) +prop_rem %<>% mutate(notpoly=case_when(som==3 & (exclude_poly+exclude_poly.2+exclude_poly.3==2) ~ 0, + som==3 & is.na(exclude_poly.2)==TRUE & (exclude_poly+exclude_poly.3==1) ~ 0, + som==3 & (exclude_poly+exclude_poly.2+exclude_poly.3==0) ~ 2, + som==3 & is.na(exclude_poly.2)==TRUE & (exclude_poly+exclude_poly.3==0) ~ 2, + som==3 & (exclude_poly+exclude_poly.2+exclude_poly.3<2) & (exclude_poly+exclude_poly.2+exclude_poly.3>0) ~ 1, + som==3 & is.na(exclude_poly.2)==TRUE & (exclude_poly+exclude_poly.3<1) & (exclude_poly+exclude_poly.3>0) ~ 1)) prop_rem %>% group_by(notpoly) %>% summarise(n=n()) ``` @@ -388,12 +379,14 @@ prop_rem %>% group_by(notpoly) %>% summarise(n=n()) #keep all markers with non mendelian prop in at least 1 dataset map_rem <- tab_alldata %>% filter(exclude_estmap==1 | exclude_estmap.2==1 | - exclude_estmap.3==1 | - exclude_estmap.4==1) + exclude_estmap.3==1) +map_rem %<>% mutate(som=case_when(exclude_match+exclude_poly+exclude_na+exclude_prop+exclude_allele+exclude_estmap==0 ~ 0, + exclude_match.2+exclude_poly.2+exclude_na.2+exclude_prop.2+exclude_allele.2+exclude_estmap.2==0 ~ 0, + exclude_match.3+exclude_poly.3+exclude_na.3+exclude_prop.3+exclude_allele.3+exclude_estmap.3==0 ~ 0,)) ``` -11/15 are okay in another cross. +5/9 are okay in another cross. diff --git a/article/data3/.RData b/article/data3/.RData index ad10895c3386d632f2830a8fdadbe074b8b70f64..2e3f9588201ca5ca711337fd7d56792c15c84ff8 100644 Binary files a/article/data3/.RData and b/article/data3/.RData differ diff --git a/article/data3/cluster/after_1000p.rda b/article/data3/cluster/after_1000p.rda index f7c7032a73d6747a961bb19e64f9a908078303c0..177f9721c88673d5e30a4c5839febd7b46cb2e26 100755 Binary files a/article/data3/cluster/after_1000p.rda and b/article/data3/cluster/after_1000p.rda differ diff --git a/article/data3/cluster/before_1000p.rda b/article/data3/cluster/before_1000p.rda index 404d5240148306fea2fd12572f2c5c9fc34d1efd..64ebb3e182265f353287e3bc64400ca739b68be6 100755 Binary files a/article/data3/cluster/before_1000p.rda and b/article/data3/cluster/before_1000p.rda differ diff --git a/article/data3/cluster/before_after.err b/article/data3/cluster/before_after.err index d5323eae115a1184f0b59400d105921c53629023..878b730c418be2fb09d6c5d18f094aea8886cc60 100755 --- a/article/data3/cluster/before_after.err +++ b/article/data3/cluster/before_after.err @@ -1,48 +1,21 @@ Warning messages: -1: In getsex(cross) : - 3 individuals with missing sex; assuming they're female -2: In fixXgeno.f2(cross, alleles) : +1: In fixXgeno.f2(cross, alleles) : --Omitting 332 male heterozygote genotypes on the X chromosome. -3: In fixXgeno.f2(cross, alleles) : +2: In fixXgeno.f2(cross, alleles) : --There appear to be some individuals of each cross direction, but "pgm" is not provided. Check the X chr genotype data and include a "pgm" column in the phenotype data. "pgm" was inferred (probably poorly). -4: In getsex(object) : - 3 individuals with missing sex; assuming they're female -5: In getsex(object) : - 3 individuals with missing sex; assuming they're female -6: In summary.cross(cross) : +3: In summary.cross(cross) : Some markers at the same position on chr 1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X; use jittermap(). Warning message: -In est.map(cross = cross_before, error.prob = 0.01) : Didn't converge! -Warning messages: -1: In matchchr(chr, names(x$geno)) : Chr Y not found -2: In getsex(cross) : - 3 individuals with missing sex; assuming they're female -3: In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, : - Dropping 3 individuals with missing phenotypes. - +In matchchr(chr, names(x$geno)) : Chr Y not found Warning messages: -1: In getsex(cross) : - 3 individuals with missing sex; assuming they're female -2: In fixXgeno.f2(cross, alleles) : +1: In fixXgeno.f2(cross, alleles) : --Omitting 27 male heterozygote genotypes on the X chromosome. -3: In fixXgeno.f2(cross, alleles) : - --There appear to be some individuals of each cross direction, but "pgm" is not provided. - Check the X chr genotype data and include a "pgm" column in the phenotype data. - "pgm" was inferred (probably poorly). - -4: In getsex(object) : - 3 individuals with missing sex; assuming they're female -5: In getsex(object) : - 3 individuals with missing sex; assuming they're female -6: In summary.cross(cross) : +2: In summary.cross(cross) : Some markers at the same position on chr 1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X; use jittermap(). -Warning messages: -1: In matchchr(chr, names(x$geno)) : Chr Y not found -2: In getsex(cross) : - 3 individuals with missing sex; assuming they're female -3: In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, : - Dropping 3 individuals with missing phenotypes. - +Warning message: +In est.map(cross = cross_after, error.prob = 0.01) : Didn't converge! +Warning message: +In matchchr(chr, names(x$geno)) : Chr Y not found diff --git a/article/data3/cluster/before_after.out b/article/data3/cluster/before_after.out index c078d977d7a104ee7a1fb15b18a11e3d370aba04..00f78b3c600828a6c16e096c4be224c9f32a5720 100755 --- a/article/data3/cluster/before_after.out +++ b/article/data3/cluster/before_after.out @@ -1,10 +1,10 @@ --Read the following data: - 92 individuals - 2774 markers + 89 individuals + 2762 markers 5 phenotypes --Cross type: f2 --Read the following data: - 92 individuals - 2630 markers + 89 individuals + 2627 markers 5 phenotypes --Cross type: f2 diff --git a/article/data3/cluster/newmap_after.rda b/article/data3/cluster/newmap_after.rda index d8f9e3c621134e360105e3336e01743ca9c1148b..ab4f2e2773a2b2872cd1c424ed9c0be591212268 100755 Binary files a/article/data3/cluster/newmap_after.rda and b/article/data3/cluster/newmap_after.rda differ diff --git a/article/data3/cluster/newmap_before.rda b/article/data3/cluster/newmap_before.rda index 15de2f094045dbeba8fcc31a10b0b3c3ab93d4b1..881845ca435a7de76e4a1d0c4fda9c20f7cb51f4 100755 Binary files a/article/data3/cluster/newmap_before.rda and b/article/data3/cluster/newmap_before.rda differ diff --git a/article/data3/data3.Rmd b/article/data3/data3.Rmd index 96ba4038d11a5c8e95481df892448b88aa8fc237..cc0c6d12e4ded854c75fd2e856a75f28f3e019cd 100644 --- a/article/data3/data3.Rmd +++ b/article/data3/data3.Rmd @@ -215,8 +215,10 @@ write_rqtl(geno=genos,pheno=phenos,tab=tab2,ref=strains,par1="StrainA",par2="Str cross_after2 <- read.cross(format="csv",file="cluster2/cross_after2.csv", genotypes=c("0","1","2"),na.strings=c("NA"), convertXdata=TRUE) -# load rda with newmap -load("cluster2/newmap_after2.rda") +cross_after2 <- calc.genoprob(cross_after2, step=2.0, off.end=0.0, + error.prob=1.0E-4, map.function="haldane", stepwidth="fixed") + +newmap_after2 <- est.map(cross=cross_after2,error.prob=0.01) # plot plotMap(cross_after2,newmap_after2,shift=TRUE) @@ -229,7 +231,9 @@ plotmap_after_data2 <- ~plotMap(cross_after_data3,newmap_after_data3,shift=TRUE, ```{r after_scan} # load rda with perm -load("cluster2/after_1000p2.rda") +after_1000p2 <- scanone(cross=cross_after2, + chr=c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "X"), + pheno.col="Pheno", model="normal", method="em", n.perm=1000, perm.Xsp=FALSE, verbose=FALSE) # calculate thresholds threshold_after <- summary(after_1000p2,alpha=c(0.05,0.1,0.63)) #donne lod score pour risque 0.05, 0.1, 0.63 @@ -361,9 +365,9 @@ chrs <- c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", " ann_dat_text<-data.frame( chr=factor(chrs, levels=chrs), - lod=c(NA,NA,NA,NA,11,NA,NA,NA,NA,13,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA), - label=c(NA,NA,NA,NA,"p4",NA,NA,NA,NA,"p5",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA), - x=c(NA,NA,NA,NA,20,NA,NA,NA,NA,27,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA) + lod=c(NA,NA,NA,NA,11,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA), + label=c(NA,NA,NA,NA,"p4",NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA), + x=c(NA,NA,NA,NA,20,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA) ) pheno_before_annot_data3 <- pheno_before_plot + geom_text( @@ -438,67 +442,6 @@ geno_plot4 <- pgmap %>% filter(pos > 1 & pos < 30) %>% geno_plot4 ``` -### Peak 5 - -```{r peak5_zoom} -peak5 <- qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1","alpha=0.63"), - lod = threshold_before[1:3]), - ylab="LOD score", - title="QTL mapping", - x.label = element_blank(), - size=0.6, - strip.pos="bottom", - chr="10", - rug=TRUE) + - theme(legend.position = "none", - strip.background = element_blank(), - strip.text.x = element_blank()) + - xlab("Position (cM)") + - xlim(c(22,42)) + - ggtitle("Peak 5: 1 marker and 1 pseudomarker") -peak5 -``` - -1 peak on 1 marker and one pseudomarker : S2C102505843 and c10.loc30 postionned between SAH102097335 and S2C102505843. - -Here are the infos on genotype counts for these markers: - -```{r summary_geno_peak5} -peak5_tab <- tab_before %>% filter(marker %in% c("SAH102097335","S2C102505843")) %>% select(marker:n_NA) -peak5_tab -``` - - -For S2C102505843, all individuals except 1 are homozygous so this marker should be removed. The proportions for SAH102097335 seem correct. - -Graph: - -```{r geno_plot_peak5} -phenotypes <- cross_before[["pheno"]] -map <- cross_before[["geno"]][["10"]][["map"]] -map <- tibble(marker=names(map),pos=map) -genotypes <- cross_before[["geno"]][["10"]][["data"]] -genotypes <- as_tibble(genotypes) -phenogeno <- cbind(phenotypes,genotypes) -phenogeno %<>% pivot_longer(gICR258:S6J105101847,names_to="marker",values_to="genotype") -pgmap <- full_join(phenogeno,map,by="marker") - -geno_plot5 <- pgmap %>% filter(pos > 25 & pos < 35) %>% - filter(id %in% sample(phenotypes$id,10)) %>% - ggplot(aes(x=pos,y=as.factor(id))) + - geom_point(aes(color=as.factor(genotype))) + - coord_cartesian(ylim = c(1, 10), expand = TRUE, clip = "off") + - annotate(geom="text",y=-1,size=3, - x = map %>% filter(pos > 25 & pos < 35) %>% pull(pos), - label = map %>% filter(pos > 25 & pos < 35) %>% pull(marker), - angle=90) + - labs(x="Position (cM)",y="Individual",color="Genotype") + - theme_bw() + - theme(plot.margin = unit(c(1, 1, 1, 1), "lines"), - axis.title.x = element_text(margin = margin(t = 50))) -geno_plot5 -``` - ## Phenotype distributions ```{r pheno_distrib} @@ -551,7 +494,7 @@ prop_plot ```{r} tab2_data3 <- tab2 -save(pheno_before_annot_data3,pheno_data3,peak5,peak5_tab,tab2_data3, +save(pheno_before_annot_data3,pheno_data3,tab2_data3, rec_ratios_before_data3,rec_ratios_after_data3, plotmap_before_data3,plotmap_after_data3, cross_before_data3,newmap_before_data3,cross_after_data3,newmap_after_data3, diff --git a/article/data3/data3.rda b/article/data3/data3.rda index 1bae884904de6b32a14eabc2b8325d56e9d029f6..67c72aef1800e7e3ae4f2765da737c1af41204b2 100644 Binary files a/article/data3/data3.rda and b/article/data3/data3.rda differ diff --git a/article/figures/fig1prev.pdf b/article/figures/fig1prev.pdf index b0f958431fd3d83cbeb436acf7d23f7c2d0de1e0..0a0158d348d03e980a9920cd5e49b90d40870830 100644 Binary files a/article/figures/fig1prev.pdf and 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