Commit 0b048313 authored by mariefbourdon's avatar mariefbourdon
Browse files

grid narrow peaks

parent 54ffd6fb
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......@@ -83,26 +83,6 @@ pheno_before_plot <- qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05"
pheno_before_plot
```
```{r before_ann}
chrs <- c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "X")
ann_dat_text<-data.frame(
chr=factor(chrs,
levels=chrs),
lod=c(rep(NA,10),8,rep(NA,9)),
label=c(rep(NA,10),7,rep(NA,9)),
x=c(rep(NA,10),22,rep(NA,9))
)
pheno_before_plot + geom_text(
# the new dataframe for annotating text
data = ann_dat_text,
mapping = aes(x = x,
y = lod,
label = label,
color="blue")
)
```
## create file for parental strains genotyped
......@@ -214,21 +194,66 @@ rm(none,allele,match,poly,prop,functions_df)
Investigation of high lod score peaks
```{r before_ann}
chrs <- c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "X")
ann_dat_text<-data.frame(
chr=factor(chrs,
levels=chrs),
lod=c(rep(NA,10),8,rep(NA,9)),
label=c(rep(NA,10),7,rep(NA,9)),
x=c(rep(NA,10),22,rep(NA,9))
)
pheno_before_annot_data2 <- pheno_before_plot + geom_text(
# the new dataframe for annotating text
data = ann_dat_text,
mapping = aes(x = x,
y = lod,
label = label,
color="blue")
)
pheno_before_annot_data2
rm(ann_dat_text)
rm(chrs)
```
### Peak 7
1 peak on 1 pseudomarker : c11.loc18, postionned between SNT111392585 and mJAX00308021.
```{r peak7_zoom}
peak7 <- 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="11",
rug=TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
xlab("Position (cM)") +
ggtitle("")
peak7
```
1 peak on chromosome 11 on 1 pseudomarker : c11.loc18, postionned between SNT111392585 and mJAX00308021.
Here are the infos on genotype counts for these markers:
```{r summary_geno_chr2}
tab_before %>% filter(marker %in% c("SNT111392585","mJAX00308021")) %>% select(marker:n_NA)
```{r summary_geno_peak7}
peak7_tab <- tab_before %>% filter(marker %in% c("SNT111392585","mJAX00308021")) %>% select(marker:n_NA)
peak7_tab
```
For SNT111392585, all individuals except 1 are homozygous so this marker should be removed. The proportions for mJAX00308021 seem correct.
Graph:
```{r geno_plot_chr2}
```{r geno_plot_peak7}
phenotypes <- cross_before[["pheno"]]
map <- cross_before[["geno"]][["11"]][["map"]]
map <- tibble(marker=names(map),pos=map)
......@@ -238,7 +263,7 @@ phenogeno <- cbind(phenotypes,genotypes)
phenogeno %<>% pivot_longer(mbackupUNC110000218:gUNC20538837,names_to="marker",values_to="genotype")
pgmap <- full_join(phenogeno,map,by="marker")
geno_plot2 <- pgmap %>% filter(pos > 15 & pos < 25) %>%
geno_plot7 <- pgmap %>% filter(pos > 15 & pos < 25) %>%
filter(id %in% sample(phenotypes$id,10)) %>%
ggplot(aes(x=pos,y=as.factor(id))) +
geom_point(aes(color=as.factor(genotype))) +
......@@ -251,7 +276,14 @@ geno_plot2 <- pgmap %>% filter(pos > 15 & pos < 25) %>%
theme_bw() +
theme(plot.margin = unit(c(1, 1, 1, 1), "lines"),
axis.title.x = element_text(margin = margin(t = 50)))
geno_plot2
geno_plot7
rm(pgmap,phenotypes,map,genotypes,phenogeno)
```
The two markers before the pseudomarker have an excess of homozygous.
```{r save_narrow}
save(pheno_before_annot_data2,peak7,peak7_tab,file="data2_peaks.rda")
```
The two markers before the pseudomarker have an excess of homozygous.
\ No newline at end of file
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......@@ -199,4 +199,11 @@ functions_plot <- functions_df %>% ggplot(aes(x=markers,y=fct)) +
functions_plot
rm(none,allele,match,poly,prop)
```
\ No newline at end of file
```
```{r}
pheno_before_data3 <- pheno_before_plot
save(pheno_before_data3,file="data3_peaks.rda")
```
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......@@ -82,25 +82,6 @@ pheno_before_plot <- qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05"
pheno_before_plot
```
```{r before_ann}
chrs <- c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "X")
ann_dat_text<-data.frame(
chr=factor(chrs,
levels=chrs),
lod=c(9,NA,NA,NA,11,NA,NA,NA,NA,13,NA,NA,8.5,NA,NA,NA,NA,7,NA,NA),
label=c(8,NA,NA,NA,9,NA,NA,NA,NA,10,NA,NA,11,NA,NA,NA,NA,12,NA,NA),
x=c(45,NA,NA,NA,20,NA,NA,NA,NA,27,NA,NA,30,NA,NA,NA,NA,35,NA,NA)
)
pheno_before_plot + geom_text(
# the new dataframe for annotating text
data = ann_dat_text,
mapping = aes(x = x,
y = lod,
label = label,
color="blue")
)
```
```{r}
#our genotypes
......@@ -225,11 +206,50 @@ rm(none,allele,match,poly,prop)
## Narrow peaks
```{r before_ann}
chrs <- c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "X")
ann_dat_text<-data.frame(
chr=factor(chrs,
levels=chrs),
lod=c(9,NA,NA,NA,11,NA,NA,NA,NA,13,NA,NA,8.5,NA,NA,NA,NA,7,NA,NA),
label=c(8,NA,NA,NA,9,NA,NA,NA,NA,10,NA,NA,11,NA,NA,NA,NA,12,NA,NA),
x=c(45,NA,NA,NA,20,NA,NA,NA,NA,27,NA,NA,30,NA,NA,NA,NA,35,NA,NA)
)
pheno_before_annot_data4 <- pheno_before_plot + geom_text(
# the new dataframe for annotating text
data = ann_dat_text,
mapping = aes(x = x,
y = lod,
label = label,
color="blue")
)
pheno_before_annot_data4
```
Investigation of high lod score peaks
### Peak 8
1 peak on 1 pseudomarker : c1.loc42, postionned between gUNC1177319 and S6J013976867.
```{r peak8_zoom}
peak8 <- 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="1",
rug=TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
xlab("Position (cM)") +
ggtitle("")
peak8
```
1 peak on chromosome 1 on 1 pseudomarker : c1.loc42, postionned between gUNC1177319 and S6J013976867.
Here are the infos on genotype counts for these markers:
......@@ -270,7 +290,25 @@ geno_plot8
### Peak 9
1 peak on 1 pseudomarker : c5.loc16, in a region with very few markers, postionned between S6J050685107 and mUNC050096588.
```{r peak9_zoom}
peak9 <- 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="5",
rug=TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
xlab("Position (cM)") +
ggtitle("")
peak9
```
1 peak on chromosome 5 on 3 pseudomarkers : c5.loc16, c5.loc18, c5.loc20 in a region with very few markers, postionned between S6J050685107 and mUNC050096588.
Here are the infos on genotype counts for these markers:
......@@ -311,7 +349,25 @@ geno_plot9
### Peak 10
1 peak on 1 pseudomarker : c10.loc30, in a region with very few markers, postionned between SAH102097335 and S2C102505843.
```{r peak10_zoom}
peak10 <- 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)") +
ggtitle("")
peak10
```
1 peak on 1 marker and one pseudomarker : S2C102505843 and c10.loc30 in a region with very few markers, postionned between SAH102097335 and S2C102505843.
Here are the infos on genotype counts for these markers:
......@@ -353,12 +409,30 @@ geno_plot10
### Peak 11
1 peak on 1 pseudomarker : c13.loc28, postionned between S6J132182752 and SAC132487883.
```{r peak11_zoom}
peak11 <- qtl_plot(pheno_before,
ylab="LOD score",
title="QTL mapping",
x.label = element_blank(),
size=0.6,
strip.pos="bottom",
chr="13",
rug=TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
xlab("Position (cM)") +
ggtitle("Peak 11")
peak11
```
1 peak on 1 marker and 1 pseudomarker : SAC132487883 and c13.loc28, postionned between S6J132182752 and SAC132487883.
Here are the infos on genotype counts for these markers:
```{r summary_geno_peak11}
tab_before %>% filter(marker %in% c("S6J132182752","SAC132487883")) %>% select(marker:n_NA)
peak11_tab <- tab_before %>% filter(marker %in% c("S6J132182752","SAC132487883")) %>% select(marker:n_NA)
peak11_tab
```
......@@ -394,6 +468,24 @@ geno_plot11
### Peak 12
```{r peak12_zoom}
peak12 <- 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="18",
rug=TRUE) +
theme(legend.position = "none",
strip.background = element_blank(),
strip.text.x = element_blank()) +
xlab("Position (cM)") +
ggtitle("")
peak12
```
1 peak on 1 marker : S3C182557441
Here are the infos on genotype counts for these markers:
......@@ -432,3 +524,9 @@ geno_plot12 <- pgmap %>% filter(pos > 32 & pos < 42) %>%
axis.title.x = element_text(margin = margin(t = 50)))
geno_plot12
```
```{r}
save(pheno_before_annot_data4,peak11,peak11_tab,file="data4_peaks.rda")
```
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