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article/.RData
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......@@ -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)
```
......
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article/data1/data1.Rmd
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......@@ -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)
```
......
article/data1/data1.rda
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article/data2/.RData
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article/data2/data2.Rmd
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......@@ -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)
```
......
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article/data3/.RData
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article/data3/data3.Rmd
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......@@ -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)
```
......
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article/figures/fig1.pdf
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article/figures/fig1prev.svg
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article/figures/fig2.pdf
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