diff --git a/article/.RData b/article/.RData
index 861d0b1fc20c480a8d65f585a49598759fdc8910..3baef568950dc68765dd9f5270f2063473358a64 100644
Binary files a/article/.RData and b/article/.RData differ
diff --git a/article/article_figures.Rmd b/article/article_figures.Rmd
index b4263f7e12bf3de7d212b66e3bcb1fafa11f6160..f26a781f23518872e37639f09ff4277837fc91fe 100644
--- a/article/article_figures.Rmd
+++ b/article/article_figures.Rmd
@@ -49,7 +49,8 @@ annot_mini <- read.csv(url("https://raw.githubusercontent.com/kbroman/MUGAarrays
```{r graph_NA}
na_plot <- tab2 %>% mutate(prop_NA=n_NA/176) %>% ggplot(aes(x=prop_NA)) +
geom_histogram() +
- scale_y_log10() +
+ scale_y_log10(expand = c(.01, .01)) +
+ scale_x_continuous(expand = c(.005, .005)) +
theme_classic() +
labs(title="Proportion of missing genotyped",
x="Proportion of NA",y="Number of markers") +
@@ -76,6 +77,8 @@ prop_plot <- tab2 %>% filter(n_NA<88) %>% filter(!chr %in% c("M","X","Y")) %>%
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) +
+ scale_x_continuous(expand = c(.005, .005)) +
+ scale_y_continuous(expand = c(.005, .005)) +
labs(title="Exclusion of markers with mark_prop()",
x="Proportion of A/A individuals",
y="Proportion of B/B individuals",
@@ -112,6 +115,8 @@ gridnaprop <- plot_grid(na_plot,prop_plot,
gridnaprop
ggsave("figures/fig2.pdf",gridnaprop,width=5,height=8)
+ggsave("figures/fig2.png",gridnaprop,width=5,height=8)
+
rm(na_plot,prop_plot)
```
@@ -125,7 +130,7 @@ rm(na_plot,prop_plot)
```{r grid_before}
grid_before <- plot_grid(as_grob(plotmap_before),rec_ratios_before,pheno_before_annot,pheno_before_zoom,ncol=2,labels=c("A","B","C","D"),label_size=20)
-
+grid_before
ggsave("figures/fig1prev.pdf",grid_before,width=14,height = 10)
```
@@ -134,7 +139,7 @@ ggsave("figures/fig1prev.pdf",grid_before,width=14,height = 10)
-```{r grid fig1, fig.height = 7, fig.width = 13, fig.align = "center"}
+```{r grid fig3, fig.height = 7, fig.width = 13, fig.align = "center"}
grid_after <- plot_grid(as_grob(plotmap_after),rec_ratios_after,pheno_after_plot,pheno_after_zoom,ncol=2,labels=c("A","B","C","D"),label_size=20)
grid_after
ggsave("figures/fig3prev.pdf",grid_after,width=14,height = 10)
@@ -304,6 +309,7 @@ ggsave(narrow_grid,file="figures/figS3prev.pdf",width=10,height=14)
```{r}
grid_mapbef <- plot_grid(plotmap_before_data2,plotmap_before_data3,rec_ratios_before_data2,rec_ratios_before_data3,ncol=2,labels=c("A","B","C","D"),label_size=20)
+grid_mapbef
ggsave("figures/figS2prev.pdf",grid_mapbef ,width=14,height = 10)
```
diff --git a/article/data1/.RData b/article/data1/.RData
index 5b31a467ad0a74720f1c7fa653b25bdb9e20f82b..001611b6e8f2f77906f7d74a218f06e9e3906e21 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 3bc0c323625d9417e4e2965fef400b9683c3274c..31231387f7cd6b72180187c96205b548f7a6cb38 100644
--- a/article/data1/data1.Rmd
+++ b/article/data1/data1.Rmd
@@ -228,11 +228,17 @@ rec_ratios_before <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
y="Count",
fill="",
title="Distance between adjacent markers") +
+ geom_vline(xintercept = 5,linetype="dashed") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
rec_ratios_before
+#percentage of markers in each group
+rec_ratios %>% mutate(group_rat=case_when(rat_prev<5 ~ 0,
+ rat_prev >=5 ~ 1)) %>%
+ group_by(group_rat) %>% summarise(n=n(),p=n()/nrow(rec_ratios))
+
rm(mark,chr,pos,place,previous,follow,kn_previous,kn_follow,fol,kn_fol,kn_pos,kn_prev,i,prev)
```
diff --git a/article/data1/data1.rda b/article/data1/data1.rda
index a1931df177353dbab88e3ad7b2c3d9931291d650..20c8cb06f2cc990e86813d1a1cd9e86bde1b4442 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 63723829a07d0744fa686fb08bcb8b8749d2509e..c7a147a98a089aa8d06666d9cec844875a62a60a 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 db7746196c77a906ab53f738e966703cb37f1dad..742a10a706bd271938bbfeb753cfff0b972faaf0 100644
--- a/article/data2/data2.Rmd
+++ b/article/data2/data2.Rmd
@@ -153,11 +153,17 @@ rec_ratios_before_data2 <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
y="Count",
fill="",
title="Distance between adjacent markers") +
+ geom_vline(xintercept = 5,linetype="dashed") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
rec_ratios_before_data2
+#percentage of markers in each group
+rec_ratios %>% mutate(group_rat=case_when(rat_prev<5 ~ 0,
+ rat_prev >=5 ~ 1)) %>%
+ group_by(group_rat) %>% summarise(n=n(),p=n()/nrow(rec_ratios))
+
rm(mark,chr,pos,place,previous,follow,kn_previous,kn_follow,fol,kn_fol,kn_pos,kn_prev,i,prev)
```
diff --git a/article/data2/data2.rda b/article/data2/data2.rda
index d81fd3487d16ba73b04d13c5ec612aa678f1aed3..525cbaca5ff2573ce023bf31e95c147bcefc44af 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 a3a92f7352ec239598f3701c79bef5c24970e54c..0c1ef1e903345bdae64c3d9964f30fee046aa489 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 94428c18ac6cbd0ddacdcbbb8d321e7d26dfec08..9abe5a0d8152e366d855846755dccd257f665dfb 100644
--- a/article/data3/data3.Rmd
+++ b/article/data3/data3.Rmd
@@ -152,11 +152,17 @@ rec_ratios_before_data3 <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
y="Count",
fill="",
title="Distance between adjacent markers") +
+ geom_vline(xintercept = 5,linetype="dashed") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(hjust=0.5,size=14))
rec_ratios_before_data3
+#percentage of markers in each group
+rec_ratios %>% mutate(group_rat=case_when(rat_prev<5 ~ 0,
+ rat_prev >=5 ~ 1)) %>%
+ group_by(group_rat) %>% summarise(n=n(),p=n()/nrow(rec_ratios))
+
rm(mark,chr,pos,place,previous,follow,kn_previous,kn_follow,fol,kn_fol,kn_pos,kn_prev,i,prev)
```
diff --git a/article/data3/data3.rda b/article/data3/data3.rda
index 6220313563745810ef4b47f7bf24bbc60476be56..c3c8007a2c91ace87ed8fc2346ab54d312ba9e96 100644
Binary files a/article/data3/data3.rda and b/article/data3/data3.rda differ
diff --git a/article/figures/fig1.pdf b/article/figures/fig1.pdf
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Binary files a/article/figures/fig1.pdf and b/article/figures/fig1.pdf differ
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new file mode 100644
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Binary files /dev/null and b/article/figures/fig1.png differ
diff --git a/article/figures/fig1prev.pdf b/article/figures/fig1prev.pdf
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Binary files a/article/figures/fig1prev.pdf and b/article/figures/fig1prev.pdf differ
diff --git a/article/figures/fig1prev.svg b/article/figures/fig1prev.svg
index dd17a147580ea8cc6857dcaef658f6d0d489d51f..a6de6e6e4dfb6470e1557d11d67214d698562694 100644
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+++ b/article/figures/fig1prev.svg
@@ -24487,6 +24487,13 @@
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id="path22112-3" />
</clipPath>
+ <clipPath
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+ id="path85254" />
+ </clipPath>
</defs>
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id="namedview20"
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+ inkscape:zoom="0.62608414"
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+ inkscape:window-width="1848"
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inkscape:window-maximized="1"
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+ inkscape:current-layer="g26">
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x="0"
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width="1344"
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- inkscape:export-filename="fig1.pdf"
+ inkscape:export-filename="fig1.png"
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