diff --git a/article/.RData b/article/.RData index e98699c949868b9ec4a46c57eb4ec9b233f0340e..7707416971adb9c17fd76c1962e608fcd5265f90 100644 Binary files a/article/.RData and b/article/.RData differ diff --git a/article/article_figures.Rmd b/article/article_figures.Rmd index f33b3457668b073084ee784808ee36e56efd34d3..d85762e7b32b476e89be10d9985790f24b46141c 100644 --- a/article/article_figures.Rmd +++ b/article/article_figures.Rmd @@ -289,21 +289,22 @@ colnames(peak5_tab) <- c("marker","chr","pos","allele\n1","allele\n2", narrow_grid <- ggdraw() + - draw_plot(pheno_before_annot_data2,.5,.8,.5,.16) + - draw_plot(pheno_before_annot_data3,0,.64,.5,.16) + - draw_plot(peak1,0,.48,.3,.16) + - draw_plot(tableGrob(peak1_tab,rows=NULL),.3,.48,.7,.16) + - draw_plot(peak3,0,.32,.3,.16) + - draw_plot(tableGrob(peak3_tab,rows=NULL),.3,.32,.7,.16) + - draw_plot(peak5,0,0,.3,.16) + - draw_plot(tableGrob(peak5_tab,rows=NULL),.3,0,.7,.16) + + 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,.5,0,.35,0,.35),c(.96,.96,.8,.8,.64,.615,.48,.45)) + c(0,.5,0,.3,0,.3,.5,.7),c(1,1,.75,.75,.5,.5,.25,.25)) narrow_grid -ggsave(narrow_grid,file="fig/figS3.pdf",width=10,height=17) +ggsave(narrow_grid,file="figures/figS3.pdf",width=10,height=17) +ggsave(narrow_grid,file="figures/figS3.png",width=10,height=17) -rm(peak1,peak1_tab,peak2,peak2_tab,peak3,peak3_tab,peak4_tab,peak5,peak5_tab,peak6,peak6_tab,peak7,peak7_tab,peak11,peak11_tab) +rm(peak1,peak1_tab,peak2,peak2_tab,peak3,peak3_tab,peak5,peak5_tab) ``` diff --git a/article/data1/.RData b/article/data1/.RData index c4e56b79e9883cdcfb94d7e842772ad34f9b85c8..2960734e065e38ddfb0be96ebde9558528ef964c 100644 Binary files a/article/data1/.RData and b/article/data1/.RData differ diff --git a/article/data1/data1.Rmd b/article/data1/data1.Rmd index a3bb3d4696c7dc2de17d71274d764970da716b0d..3b6b6829f5a35ac02ebcce206d9bd43532c326f7 100644 --- a/article/data1/data1.Rmd +++ b/article/data1/data1.Rmd @@ -426,7 +426,7 @@ peak1 <- qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1 strip.text.x = element_blank()) + xlab("Position (cM)") + xlim(c(15,35)) + - ggtitle("Peak 1") + ggtitle("Peak 1: 1 marker") peak1 ``` diff --git a/article/data1/data1.rda b/article/data1/data1.rda index ce8e4bd07cfb88cf186c9dea318ed9cc1c8f344d..7b52e74023001f64b76dc04ca52f74224bacca23 100644 Binary files a/article/data1/data1.rda and b/article/data1/data1.rda differ diff --git a/article/data2/.RData b/article/data2/.RData index e45601ea57fb6bcbe5515d84cc4ab6999187da71..d96aa25a90287e3653ab4f547d42768f2e2872d5 100644 Binary files a/article/data2/.RData and b/article/data2/.RData differ diff --git a/article/data2/data2.Rmd b/article/data2/data2.Rmd index 4a04e28176c201fb3c6660777e9dbf4f2a195a84..a140a19931d26f6a5e0ae9ab7fbfc2671e12f52a 100644 --- a/article/data2/data2.Rmd +++ b/article/data2/data2.Rmd @@ -363,7 +363,8 @@ pheno_before_annot_data2 <- pheno_before_plot + geom_text( y = lod, label = label, color="blue") -) + ) + + ggtitle("Data 2") pheno_before_annot_data2 rm(ann_dat_text) @@ -388,7 +389,7 @@ peak3 <- qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1 strip.text.x = element_blank()) + xlab("Position (cM)") + xlim(c(11,31)) + - ggtitle("Peak 3") + ggtitle("Peak 3: 1 pseudomarker") peak3 ``` @@ -448,6 +449,46 @@ pheno_data2 <- phenos %>% ggplot(aes(x=Pheno)) + pheno_data2 ``` +## Missing genotypes + +```{r} +na_plot <- tab2 %>% mutate(prop_NA=n_NA/176) %>% ggplot(aes(x=prop_NA)) + + geom_histogram() + + scale_y_log10() + + theme_classic() + + labs(title="Proportion of missing genotyped", + x="Proportion of NA",y="Number of markers") + + theme( + aspect.ratio=0.8, + plot.title = element_text(hjust = 0.4,face="bold",size=14)) + +na_plot +``` + +## Genotype proportions + +```{r} +prop_plot <- tab2 %>% filter(n_NA<88) %>% filter(!chr %in% c("M","X","Y")) %>% + ggplot(aes(x=n_HM1/(n_HM1+n_HM2+n_HT),y=n_HM2/(n_HM1+n_HM2+n_HT),color=as.factor(exclude_prop))) + + geom_point() + + scale_color_manual(values=c("#66bd63","#b2182b"),labels = c("Retained", "Excluded")) + + geom_hline(yintercept = 0.1,linetype="dashed",size=.3) + + geom_vline(xintercept = 0.1,linetype="dashed",size=.3) + + geom_abline(intercept = 0.9, slope=-1,linetype="dashed",size=.3) + + labs(title="Exclusion of markers with mark_prop()", + x="Proportion of homozygous individuals AA", + y="Proportion of homozygous individuals BB", + color="Exclusion") + + theme_classic() + + theme(aspect.ratio=0.8, + legend.position=c(0.8,0.8), + legend.title = element_blank()) + + theme(plot.title = element_text(hjust = 0.4,face="bold",size=14)) + +prop_plot +``` + + ```{r save_narrow} tab2_data2 <- tab2 save(pheno_before_annot_data2,pheno_data2,peak3,peak3_tab,tab2_data2, diff --git a/article/data2/data2.rda b/article/data2/data2.rda index 71008b9bfc001c84249cf18ecfcdaca658f12d23..82298732fdfd63549aea0badd642c61a3a6f0759 100644 Binary files a/article/data2/data2.rda and b/article/data2/data2.rda differ diff --git a/article/data3/.RData b/article/data3/.RData index 7d39fc8ef76a1245bf928e72e768c13c9b9e0b49..5431637c11b1d396a7f99d780671978f859934f8 100644 Binary files a/article/data3/.RData and b/article/data3/.RData differ diff --git a/article/data3/data3.Rmd b/article/data3/data3.Rmd index 6f43e5a2efe3f01fadf7e642d84a697df59b74c6..96ba4038d11a5c8e95481df892448b88aa8fc237 100644 --- a/article/data3/data3.Rmd +++ b/article/data3/data3.Rmd @@ -373,7 +373,8 @@ pheno_before_annot_data3 <- pheno_before_plot + geom_text( y = lod, label = label, color="blue") -) + ) + + ggtitle("Data 3") pheno_before_annot_data3 ``` @@ -454,7 +455,7 @@ peak5 <- qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1 strip.text.x = element_blank()) + xlab("Position (cM)") + xlim(c(22,42)) + - ggtitle("") + ggtitle("Peak 5: 1 marker and 1 pseudomarker") peak5 ``` @@ -509,6 +510,44 @@ pheno_data3 <- phenos %>% ggplot(aes(x=Pheno)) + pheno_data3 ``` +## Missing genotypes + +```{r} +na_plot <- tab2 %>% mutate(prop_NA=n_NA/176) %>% ggplot(aes(x=prop_NA)) + + geom_histogram() + + scale_y_log10() + + theme_classic() + + labs(title="Proportion of missing genotyped", + x="Proportion of NA",y="Number of markers") + + theme( + aspect.ratio=0.8, + plot.title = element_text(hjust = 0.4,face="bold",size=14)) + +na_plot +``` + +## Genotype proportions + +```{r} +prop_plot <- tab2 %>% filter(n_NA<88) %>% filter(!chr %in% c("M","X","Y")) %>% + ggplot(aes(x=n_HM1/(n_HM1+n_HM2+n_HT),y=n_HM2/(n_HM1+n_HM2+n_HT),color=as.factor(exclude_prop))) + + geom_point() + + scale_color_manual(values=c("#66bd63","#b2182b"),labels = c("Retained", "Excluded")) + + geom_hline(yintercept = 0.1,linetype="dashed",size=.3) + + geom_vline(xintercept = 0.1,linetype="dashed",size=.3) + + geom_abline(intercept = 0.9, slope=-1,linetype="dashed",size=.3) + + labs(title="Exclusion of markers with mark_prop()", + x="Proportion of homozygous individuals AA", + y="Proportion of homozygous individuals BB", + color="Exclusion") + + theme_classic() + + theme(aspect.ratio=0.8, + legend.position=c(0.8,0.8), + legend.title = element_blank()) + + theme(plot.title = element_text(hjust = 0.4,face="bold",size=14)) + +prop_plot +``` ```{r} tab2_data3 <- tab2 diff --git a/article/data3/data3.rda b/article/data3/data3.rda index 3110c1c0b98bdf872b7a625177a2699ffef03402..1bae884904de6b32a14eabc2b8325d56e9d029f6 100644 Binary files a/article/data3/data3.rda and b/article/data3/data3.rda differ diff --git a/article/figures/figS3.pdf b/article/figures/figS3.pdf new file mode 100644 index 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id="g6409" /> + <g + id="g6411" /> + <g + id="g6413" /> + <g + id="g6415" /> + <g + id="g6417" /> + <g + id="g6419" /> + <g + id="g6421" /> + <g + id="g6423" /> + <g + id="g6425" /> + <g + id="g6427" /> + <g + id="g6429" /> + <g + id="g6431" /> + <g + id="g6433" /> + <text + xml:space="preserve" + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:11.5926px;font-family:Helvetica;-inkscape-font-specification:'Helvetica, Bold';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;fill:#000000;stroke-width:0.735505" + x="47.252171" + y="-604.6192" + id="text6879" + transform="scale(0.98812383,-1.0120189)"><tspan + sodipodi:role="line" + id="tspan6877" + style="stroke-width:0.735505" + x="47.252171" + y="-604.6192">Case 2: one pseudomarker (peaks 3 and 4)</tspan></text> + <text + xml:space="preserve" + style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-size:11.5926px;font-family:Helvetica;-inkscape-font-specification:'Helvetica, Bold';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;fill:#000000;stroke-width:0.735505" + x="47.252411" + y="-292.81949" + id="text6879-4" + transform="scale(0.98812383,-1.0120189)"><tspan + sodipodi:role="line" + style="stroke-width:0.735505" + x="47.252411" + y="-292.81949" + id="tspan6916">Case 3: one marker and one pseudomarker (peak 5)</tspan></text> + <rect + style="fill:#ff0000;stroke-width:0.731478" + id="rect10188" + width="0.93699521" + height="7.4201827" + x="125.51591" + y="-653.63171" + transform="scale(1,-1)" /> + <rect + style="fill:#ff0000;stroke-width:0.731478" + id="rect10188-0" + width="0.93699521" + height="7.4201827" + x="128.18433" + y="-343.4881" + transform="scale(1,-1)" /> + <rect + style="fill:#ff0000;stroke-width:0.731478" + 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