diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
index 033fd27363a6431dd5faaf16a0e102d6bf55ce6e..63b87f60b490fabe6fade435ffb96cbfd531e4c4 100644
--- a/.Rproj.user/shared/notebooks/paths
+++ b/.Rproj.user/shared/notebooks/paths
@@ -1,4 +1,5 @@
/home/marie/Documents/HB_CC011/F2/Geno/Maestro/F2_geno_estmap1.R="42B0AE06"
+/home/marie/Documents/stuart/stuart_package/stuart/DESCRIPTION="55556B0B"
/home/marie/Documents/stuart/stuart_package/stuart/R/mark_estmap.R="F759F000"
/home/marie/Documents/stuart/stuart_package/stuart/README.Rmd="4E06E7DC"
/home/marie/Documents/stuart/stuart_package/stuart/vignettes/stuart.Rmd="01396A37"
diff --git a/article/article_figures.Rmd b/article/article_figures.Rmd
index fd16965990203d0c0d5785c170c6a1b3f727f890..3274d5f361e5af45dbaa11ce4024bef0182cbc0a 100644
--- a/article/article_figures.Rmd
+++ b/article/article_figures.Rmd
@@ -115,7 +115,7 @@ tab2 <- mark_estmap(tab=tab2,map=stuart_newmap,annot=annot_mini)
na_plot <- tab2 %>% mutate(prop_NA=n_NA/176) %>% ggplot(aes(x=prop_NA)) +
geom_histogram() +
scale_y_log10() +
- theme_bw() +
+ theme_classic() +
labs(title="Proportion of missing genotyped",
x="Proportion of NA",y="Number of markers") +
theme(
@@ -138,6 +138,9 @@ 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) +
#geom_text(aes(label=ifelse(exclude_prop=="1",SNP.Name,'')),hjust=0, vjust=0,size=2) +
labs(title="Exclusion of markers with mark_prop()",
x="Proportion of homozygous individuals AA",
@@ -148,14 +151,14 @@ prop_plot <- tab2 %>% filter(n_NA<88) %>% filter(!chr %in% c("M","X","Y")) %>%
legend.position=c(0.8,0.8),
legend.title = element_blank()) +
theme(plot.title = element_text(hjust = 0.4,face="bold",size=14)) +
- geom_segment(x = 0.2, y = 0.82,
+ geom_segment(x = 0.2, y = 0.78,
xend = 0.25, yend = 0.72,
color = "#1d91c0",
- arrow = arrow(type="closed",length=unit(6,"points"))) +
- geom_segment(x = 0.39, y = 0.62,
+ arrow = arrow(type="closed",length=unit(4,"points"))) +
+ geom_segment(x = 0.39, y = 0.58,
xend = 0.44, yend = 0.52,
color = "#1d91c0",
- arrow = arrow(type="closed",length=unit(6,"points")))
+ arrow = arrow(type="closed",length=unit(4,"points")))
prop_plot
```
### Grid
@@ -207,7 +210,7 @@ load("files/cluster/newmap_before.rda")
# plot
plotMap(cross_before,newmap_before,shift=TRUE)
-plotmap_before <- ~plotMap(cross_before,newmap_before,shift=TRUE,main="Before stuart", ylab='^')
+plotmap_before <- ~plotMap(cross_before,newmap_before,shift=TRUE,main="Before stuart", ylab='')
```
### Before: plot genome scan
@@ -247,10 +250,12 @@ pheno_before_plot
pheno_before_zoom <- 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",
chrs = "13",
size=0.6) +
- theme(legend.position = "none") +
+ theme(legend.position = "none",
+ strip.background = element_blank(),
+ strip.text.x = element_blank()) +
+ xlab("Position (cM)") +
ggtitle("")
pheno_before_zoom
```
@@ -345,7 +350,8 @@ pheno_after_plot <- qtl_plot(pheno_after,lod=data.frame(group = c("alpha=0.05",
ylab="LOD score",
title="QTL mapping",
x.label = element_blank(),
- size=0.6) +
+ size=0.6,
+ strip.pos="bottom") +
theme(legend.position = "none") +
ggtitle("")
pheno_after_plot
diff --git a/article/figures/fig1.pdf b/article/figures/fig1.pdf
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diff --git a/article/figures/fig2.pdf b/article/figures/fig2.pdf
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diff --git a/article/figures/fig3.pdf b/article/figures/fig3.pdf
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diff --git a/article/tables/tab_alleles.tex b/article/tables/tab_alleles.tex
index a3b393a4572c90e815405f68c25c7e22d1c8e0b7..2bb108ae7e4773700e70e78f3058464a890c2dff 100644
--- a/article/tables/tab_alleles.tex
+++ b/article/tables/tab_alleles.tex
@@ -1,17 +1,17 @@
-% latex table generated in R 4.0.4 by xtable 1.8-4 package
-% Tue Feb 15 09:50:40 2022
+% latex table generated in R 4.1.0 by xtable 1.8-4 package
+% Thu Jun 9 11:29:15 2022
\begin{table}[ht]
\centering
-\begin{tabular}{lllll}
+\begin{tabular}{llrr}
\hline
-marker & parent1 & parent2 & allele\_1 & allele\_2 \\
+Ind & Sex & Age & Pheno \\
\hline
-S6J017555686 & C & C & T & C \\
- S6J113080150 & G & G & A & G \\
- gJAX00038569 & C & C & T & C \\
- mUNC21540855 & C & C & A & C \\
- gUNC21555204 & T & T & T & C \\
- gUNC21596600 & A & A & A & G \\
+201 & M & 7 & 10.53 \\
+ 210 & M & 7 & 10.49 \\
+ 308 & F & 7 & 10.97 \\
+ 309 & M & 7 & 10.85 \\
+ 310 & M & 7 & 11.07 \\
+ 311 & F & 9 & 10.58 \\
\hline
\end{tabular}
\end{table}