Commit c792484b authored by mariefbourdon's avatar mariefbourdon
Browse files

220705 figures

parent 38a353b5
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......@@ -52,7 +52,7 @@ na_plot <- tab2 %>% mutate(prop_NA=n_NA/176) %>% ggplot(aes(x=prop_NA)) +
scale_y_log10(expand = c(.01, .01)) +
scale_x_continuous(expand = c(.005, .005)) +
theme_classic() +
labs(title="Proportion of missing genotyped",
labs(title="Proportion of missing genotypes",
x="Proportion of NA",y="Number of markers") +
theme(
aspect.ratio=0.8,
......@@ -79,7 +79,7 @@ prop_plot <- tab2 %>% filter(n_NA<88) %>% filter(!chr %in% c("M","X","Y")) %>%
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()",
labs(title="Exclusion of markers by mark_prop()",
x="Proportion of A/A individuals",
y="Proportion of B/B individuals",
color="Exclusion") +
......
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......@@ -224,10 +224,10 @@ rec_ratios %>% summarise(mean=mean(rat_prev,na.rm=TRUE),
rec_ratios_before <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
geom_histogram(binwidth = .1,alpha=0.4, position="identity",fill="#990000") +
scale_x_log10(limits=c(0.2,1000)) +
labs(x="Ratio between the calculated and the known distance with the previous marker",
y="Count",
labs(x="Ratio between the calculated and the known distances",
y="Marker pairs",
fill="",
title="Distance between adjacent markers") +
title="Distances between adjacent markers") +
geom_vline(xintercept = 5,linetype="dashed") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
......@@ -327,6 +327,49 @@ plotMap(cross_after2,newmap_after2,shift=TRUE)
plotmap_after <- ~plotMap(cross_after2,newmap_after2,shift=TRUE,main="")
```
### map length
```{r}
#calc map
length_calc <- newmap_after2[["1"]][[length(newmap_after2[["1"]])]] + newmap_after2[["2"]][[length(newmap_after2[["2"]])]] +
newmap_after2[["3"]][[length(newmap_after2[["3"]])]] + newmap_after2[["4"]][[length(newmap_after2[["4"]])]] +
newmap_after2[["5"]][[length(newmap_after2[["5"]])]] + newmap_after2[["6"]][[length(newmap_after2[["6"]])]] +
newmap_after2[["7"]][[length(newmap_after2[["7"]])]] + newmap_after2[["8"]][[length(newmap_after2[["8"]])]] +
newmap_after2[["9"]][[length(newmap_after2[["9"]])]] + newmap_after2[["10"]][[length(newmap_after2[["10"]])]] +
newmap_after2[["11"]][[length(newmap_after2[["11"]])]] + newmap_after2[["12"]][[length(newmap_after2[["12"]])]] +
newmap_after2[["13"]][[length(newmap_after2[["13"]])]] + newmap_after2[["14"]][[length(newmap_after2[["14"]])]] +
newmap_after2[["15"]][[length(newmap_after2[["15"]])]] + newmap_after2[["16"]][[length(newmap_after2[["16"]])]] +
newmap_after2[["17"]][[length(newmap_after2[["17"]])]] + newmap_after2[["18"]][[length(newmap_after2[["18"]])]] +
newmap_after2[["19"]][[length(newmap_after2[["19"]])]] + newmap_after2[["X"]][[length(newmap_after2[["X"]])]]
#known map
lengh_known <- cross_after2[["geno"]][["1"]][["map"]][[length(cross_after2[["geno"]][["1"]][["map"]])]] +
cross_after2[["geno"]][["2"]][["map"]][[length(cross_after2[["geno"]][["2"]][["map"]])]] +
cross_after2[["geno"]][["3"]][["map"]][[length(cross_after2[["geno"]][["3"]][["map"]])]] +
cross_after2[["geno"]][["4"]][["map"]][[length(cross_after2[["geno"]][["4"]][["map"]])]] +
cross_after2[["geno"]][["5"]][["map"]][[length(cross_after2[["geno"]][["5"]][["map"]])]] +
cross_after2[["geno"]][["6"]][["map"]][[length(cross_after2[["geno"]][["6"]][["map"]])]] +
cross_after2[["geno"]][["7"]][["map"]][[length(cross_after2[["geno"]][["7"]][["map"]])]] +
cross_after2[["geno"]][["8"]][["map"]][[length(cross_after2[["geno"]][["8"]][["map"]])]] +
cross_after2[["geno"]][["9"]][["map"]][[length(cross_after2[["geno"]][["9"]][["map"]])]] +
cross_after2[["geno"]][["10"]][["map"]][[length(cross_after2[["geno"]][["10"]][["map"]])]] +
cross_after2[["geno"]][["11"]][["map"]][[length(cross_after2[["geno"]][["11"]][["map"]])]] +
cross_after2[["geno"]][["12"]][["map"]][[length(cross_after2[["geno"]][["12"]][["map"]])]] +
cross_after2[["geno"]][["13"]][["map"]][[length(cross_after2[["geno"]][["13"]][["map"]])]] +
cross_after2[["geno"]][["14"]][["map"]][[length(cross_after2[["geno"]][["14"]][["map"]])]] +
cross_after2[["geno"]][["15"]][["map"]][[length(cross_after2[["geno"]][["15"]][["map"]])]] +
cross_after2[["geno"]][["16"]][["map"]][[length(cross_after2[["geno"]][["16"]][["map"]])]] +
cross_after2[["geno"]][["17"]][["map"]][[length(cross_after2[["geno"]][["17"]][["map"]])]] +
cross_after2[["geno"]][["18"]][["map"]][[length(cross_after2[["geno"]][["18"]][["map"]])]] +
cross_after2[["geno"]][["19"]][["map"]][[length(cross_after2[["geno"]][["19"]][["map"]])]] +
cross_after2[["geno"]][["X"]][["map"]][[length(cross_after2[["geno"]][["X"]][["map"]])]]
#ratio
length_rat <- length_calc/lengh_known
length_rat
```
### After: plot genome scan
```{r after_scan}
......@@ -369,7 +412,7 @@ pheno_after_zoom <- qtl_plot(pheno_after,lod=data.frame(group = c("alpha=0.05",
strip.background = element_blank(),
strip.text.x = element_blank()) +
xlab("Position (cM)") +
ggtitle("QTL") +
ggtitle("Chromosome 12 QTL") +
theme(plot.title = element_text(face="plain",size=14))
pheno_after_zoom
```
......@@ -433,10 +476,10 @@ rec_ratios %>% summarise(mean=mean(rat_prev,na.rm=TRUE),
rec_ratios_after <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
geom_histogram(binwidth = .1,alpha=0.4, position="identity",fill="#2171b5") +
scale_x_log10(limits=c(0.2,1000)) +
labs(x="Ratio between the calculated and the known distance with the previous marker",
y="Count",
labs(x="Ratio between the calculated and the known distances",
y="Marker pairs",
fill="",
title="Distance between adjacent markers") +
title="Distances between adjacent markers") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
......@@ -614,7 +657,7 @@ test_plot
pheno_data1 <- phenos %>% ggplot(aes(x=Pheno)) +
geom_histogram(binwidth=0.1) +
ggpubr::theme_classic2() +
labs(y="Count", x="Quantitative phenotype",title="Dataset 1") +
labs(y="F2 individuals", x="Quantitative phenotype",title="Dataset 1") +
theme(plot.title = element_text(hjust=0.5,size=14))
pheno_data1
```
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......@@ -149,10 +149,10 @@ rec_ratios %>% summarise(mean=mean(rat_prev,na.rm=TRUE),
rec_ratios_before_data2 <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
geom_histogram(binwidth = .1,alpha=0.4, position="identity",fill="#990000") +
scale_x_log10(limits=c(0.2,1000)) +
labs(x="Ratio between the calculated and the known distance with the previous marker",
y="Count",
labs(x="Ratio between the calculated and the known distances",
y="Marker pairs",
fill="",
title="Distance between adjacent markers") +
title="Distances between adjacent markers") +
geom_vline(xintercept = 5,linetype="dashed") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
......@@ -164,6 +164,13 @@ 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))
#meansd of peak <5
rec_ratios %>% filter(rat_prev<5) %>% summarise(mean=mean(rat_prev),
sd=sd(rat_prev))
#max ratio
rec_ratios %>% summarise(max=max(rat_prev))
rm(mark,chr,pos,place,previous,follow,kn_previous,kn_follow,fol,kn_fol,kn_pos,kn_prev,i,prev)
```
......@@ -221,6 +228,47 @@ plotmap_after_data2 <- ~plotMap(cross_after_data2,newmap_after_data2,shift=TRUE,
tab2 <- mark_estmap(tab=tab2,map=newmap_after,annot=annot_mini) #0 marker removed
```
### map length
```{r}
#calc map
length_calc <- newmap_after[["1"]][[length(newmap_after[["1"]])]] + newmap_after[["2"]][[length(newmap_after[["2"]])]] +
newmap_after[["3"]][[length(newmap_after[["3"]])]] + newmap_after[["4"]][[length(newmap_after[["4"]])]] +
newmap_after[["5"]][[length(newmap_after[["5"]])]] + newmap_after[["6"]][[length(newmap_after[["6"]])]] +
newmap_after[["7"]][[length(newmap_after[["7"]])]] + newmap_after[["8"]][[length(newmap_after[["8"]])]] +
newmap_after[["9"]][[length(newmap_after[["9"]])]] + newmap_after[["10"]][[length(newmap_after[["10"]])]] +
newmap_after[["11"]][[length(newmap_after[["11"]])]] + newmap_after[["12"]][[length(newmap_after[["12"]])]] +
newmap_after[["13"]][[length(newmap_after[["13"]])]] + newmap_after[["14"]][[length(newmap_after[["14"]])]] +
newmap_after[["15"]][[length(newmap_after[["15"]])]] + newmap_after[["16"]][[length(newmap_after[["16"]])]] +
newmap_after[["17"]][[length(newmap_after[["17"]])]] + newmap_after[["18"]][[length(newmap_after[["18"]])]] +
newmap_after[["19"]][[length(newmap_after[["19"]])]] + newmap_after[["X"]][[length(newmap_after[["X"]])]]
#known map
lengh_known <- cross_after[["geno"]][["1"]][["map"]][[length(cross_after[["geno"]][["1"]][["map"]])]] +
cross_after[["geno"]][["2"]][["map"]][[length(cross_after[["geno"]][["2"]][["map"]])]] +
cross_after[["geno"]][["3"]][["map"]][[length(cross_after[["geno"]][["3"]][["map"]])]] +
cross_after[["geno"]][["4"]][["map"]][[length(cross_after[["geno"]][["4"]][["map"]])]] +
cross_after[["geno"]][["5"]][["map"]][[length(cross_after[["geno"]][["5"]][["map"]])]] +
cross_after[["geno"]][["6"]][["map"]][[length(cross_after[["geno"]][["6"]][["map"]])]] +
cross_after[["geno"]][["7"]][["map"]][[length(cross_after[["geno"]][["7"]][["map"]])]] +
cross_after[["geno"]][["8"]][["map"]][[length(cross_after[["geno"]][["8"]][["map"]])]] +
cross_after[["geno"]][["9"]][["map"]][[length(cross_after[["geno"]][["9"]][["map"]])]] +
cross_after[["geno"]][["10"]][["map"]][[length(cross_after[["geno"]][["10"]][["map"]])]] +
cross_after[["geno"]][["11"]][["map"]][[length(cross_after[["geno"]][["11"]][["map"]])]] +
cross_after[["geno"]][["12"]][["map"]][[length(cross_after[["geno"]][["12"]][["map"]])]] +
cross_after[["geno"]][["13"]][["map"]][[length(cross_after[["geno"]][["13"]][["map"]])]] +
cross_after[["geno"]][["14"]][["map"]][[length(cross_after[["geno"]][["14"]][["map"]])]] +
cross_after[["geno"]][["15"]][["map"]][[length(cross_after[["geno"]][["15"]][["map"]])]] +
cross_after[["geno"]][["16"]][["map"]][[length(cross_after[["geno"]][["16"]][["map"]])]] +
cross_after[["geno"]][["17"]][["map"]][[length(cross_after[["geno"]][["17"]][["map"]])]] +
cross_after[["geno"]][["18"]][["map"]][[length(cross_after[["geno"]][["18"]][["map"]])]] +
cross_after[["geno"]][["19"]][["map"]][[length(cross_after[["geno"]][["19"]][["map"]])]] +
cross_after[["geno"]][["X"]][["map"]][[length(cross_after[["geno"]][["X"]][["map"]])]]
#ratio
length_rat <- length_calc/lengh_known
length_rat
```
```{r after_scan}
# load rda with perm
......@@ -243,7 +291,8 @@ pheno_after_plot_data2 <- qtl_plot(pheno_after,lod=data.frame(group = c("alpha=0
ylab="LOD score",
title="QTL mapping",
x.label = element_blank(),
size=0.6) +
size=0.6,
strip.pos="bottom") +
theme(legend.position = "none") +
ggtitle("Dataset 2: genome scan") +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
......@@ -338,10 +387,10 @@ rec_ratios %>% summarise(mean=mean(rat_prev,na.rm=TRUE),
rec_ratios_after_data2 <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
geom_histogram(binwidth = .1,alpha=0.4, position="identity",fill="#2171b5") +
scale_x_log10(limits=c(0.2,1000)) +
labs(x="Ratio between the calculated and the known distance with the previous marker",
y="Count",
labs(x="Ratio between the calculated and the known distances",
y="Marker pairs",
fill="",
title="Distance between adjacent markers") +
title="Distances between adjacent markers") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
......@@ -383,7 +432,7 @@ rm(chrs)
### Peak 3
grid_scans
```{r peak3_zoom}
peak3 <- qtl_plot(pheno_before,lod=data.frame(group = c("alpha=0.05", "alpha=0.1","alpha=0.63"),
lod = threshold_before[1:3]),
......@@ -454,7 +503,7 @@ The two markers before the pseudomarker have an excess of homozygous.
pheno_data2 <- phenos %>% ggplot(aes(x=Pheno)) +
geom_histogram(binwidth=0.1) +
ggpubr::theme_classic2() +
labs(y="Count", x="Quantitative phenotype",title="Dataset 2") +
labs(y="F2 individuals", x="Quantitative phenotype",title="Dataset 2") +
theme(plot.title = element_text(hjust=0.5,size=14))
pheno_data2
```
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......@@ -148,10 +148,10 @@ rec_ratios %>% summarise(mean=mean(rat_prev,na.rm=TRUE),
rec_ratios_before_data3 <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
geom_histogram(binwidth = .1,alpha=0.4, position="identity",fill="#990000") +
scale_x_log10(limits=c(0.2,1000)) +
labs(x="Ratio between the calculated and the known distance with the previous marker",
y="Count",
labs(x="Ratio between the calculated and the known distances",
y="Marker pairs",
fill="",
title="Distance between adjacent markers") +
title="Distances between adjacent markers") +
geom_vline(xintercept = 5,linetype="dashed") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(hjust=0.5,size=14))
......@@ -266,6 +266,48 @@ newmap_after_data3 <- newmap_after2
plotmap_after_data3 <- ~plotMap(cross_after_data3,newmap_after_data3,shift=TRUE,main="")
```
### map length
```{r}
#calc map
length_calc <- newmap_after2[["1"]][[length(newmap_after2[["1"]])]] + newmap_after2[["2"]][[length(newmap_after2[["2"]])]] +
newmap_after2[["3"]][[length(newmap_after2[["3"]])]] + newmap_after2[["4"]][[length(newmap_after2[["4"]])]] +
newmap_after2[["5"]][[length(newmap_after2[["5"]])]] + newmap_after2[["6"]][[length(newmap_after2[["6"]])]] +
newmap_after2[["7"]][[length(newmap_after2[["7"]])]] + newmap_after2[["8"]][[length(newmap_after2[["8"]])]] +
newmap_after2[["9"]][[length(newmap_after2[["9"]])]] + newmap_after2[["10"]][[length(newmap_after2[["10"]])]] +
newmap_after2[["11"]][[length(newmap_after2[["11"]])]] + newmap_after2[["12"]][[length(newmap_after2[["12"]])]] +
newmap_after2[["13"]][[length(newmap_after2[["13"]])]] + newmap_after2[["14"]][[length(newmap_after2[["14"]])]] +
newmap_after2[["15"]][[length(newmap_after2[["15"]])]] + newmap_after2[["16"]][[length(newmap_after2[["16"]])]] +
newmap_after2[["17"]][[length(newmap_after2[["17"]])]] + newmap_after2[["18"]][[length(newmap_after2[["18"]])]] +
newmap_after2[["19"]][[length(newmap_after2[["19"]])]] + newmap_after2[["X"]][[length(newmap_after2[["X"]])]]
#known map
lengh_known <- cross_after2[["geno"]][["1"]][["map"]][[length(cross_after2[["geno"]][["1"]][["map"]])]] +
cross_after2[["geno"]][["2"]][["map"]][[length(cross_after2[["geno"]][["2"]][["map"]])]] +
cross_after2[["geno"]][["3"]][["map"]][[length(cross_after2[["geno"]][["3"]][["map"]])]] +
cross_after2[["geno"]][["4"]][["map"]][[length(cross_after2[["geno"]][["4"]][["map"]])]] +
cross_after2[["geno"]][["5"]][["map"]][[length(cross_after2[["geno"]][["5"]][["map"]])]] +
cross_after2[["geno"]][["6"]][["map"]][[length(cross_after2[["geno"]][["6"]][["map"]])]] +
cross_after2[["geno"]][["7"]][["map"]][[length(cross_after2[["geno"]][["7"]][["map"]])]] +
cross_after2[["geno"]][["8"]][["map"]][[length(cross_after2[["geno"]][["8"]][["map"]])]] +
cross_after2[["geno"]][["9"]][["map"]][[length(cross_after2[["geno"]][["9"]][["map"]])]] +
cross_after2[["geno"]][["10"]][["map"]][[length(cross_after2[["geno"]][["10"]][["map"]])]] +
cross_after2[["geno"]][["11"]][["map"]][[length(cross_after2[["geno"]][["11"]][["map"]])]] +
cross_after2[["geno"]][["12"]][["map"]][[length(cross_after2[["geno"]][["12"]][["map"]])]] +
cross_after2[["geno"]][["13"]][["map"]][[length(cross_after2[["geno"]][["13"]][["map"]])]] +
cross_after2[["geno"]][["14"]][["map"]][[length(cross_after2[["geno"]][["14"]][["map"]])]] +
cross_after2[["geno"]][["15"]][["map"]][[length(cross_after2[["geno"]][["15"]][["map"]])]] +
cross_after2[["geno"]][["16"]][["map"]][[length(cross_after2[["geno"]][["16"]][["map"]])]] +
cross_after2[["geno"]][["17"]][["map"]][[length(cross_after2[["geno"]][["17"]][["map"]])]] +
cross_after2[["geno"]][["18"]][["map"]][[length(cross_after2[["geno"]][["18"]][["map"]])]] +
cross_after2[["geno"]][["19"]][["map"]][[length(cross_after2[["geno"]][["19"]][["map"]])]] +
cross_after2[["geno"]][["X"]][["map"]][[length(cross_after2[["geno"]][["X"]][["map"]])]]
#ratio
length_rat <- length_calc/lengh_known
length_rat
```
```{r after_scan}
# load rda with perm
after_1000p2 <- scanone(cross=cross_after2,
......@@ -289,7 +331,8 @@ pheno_after_plot_data3 <- qtl_plot(pheno_after,lod=data.frame(group = c("alpha=0
ylab="LOD score",
title="QTL mapping",
x.label = element_blank(),
size=0.6) +
size=0.6,
strip.pos="bottom") +
theme(legend.position = "none") +
ggtitle("Dataset 3: genome scan") +
theme(plot.title = element_text(face="plain",size=14,hjust=0.5))
......@@ -355,10 +398,10 @@ rec_ratios %>% summarise(mean=mean(rat_prev,na.rm=TRUE),
rec_ratios_after_data3 <- rec_ratios %>% ggplot(aes(x=rat_prev)) +
geom_histogram(binwidth = .1,alpha=0.4, position="identity",fill="#2171b5") +
scale_x_log10(limits=c(0.2,1000)) +
labs(x="Ratio between the calculated and the known distance with the previous marker",
y="Count",
labs(x="Ratio between the calculated and the known distances",
y="Marker pairs",
fill="",
title="Distance between adjacent markers") +
title="Distances between adjacent markers") +
ggpubr::theme_classic2() +
theme(plot.title = element_text(hjust=0.5,size=14))
......@@ -488,7 +531,7 @@ geno_plot4
pheno_data3 <- phenos %>% ggplot(aes(x=Pheno)) +
geom_histogram(binwidth=0.2) +
ggpubr::theme_classic2() +
labs(y="Count", x="Quantitative phenotype",title="Dataset 3") +
labs(y="F2 individuals", x="Quantitative phenotype",title="Dataset 3") +
theme(plot.title = element_text(hjust=0.5,size=14))
pheno_data3
```
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......@@ -24505,9 +24505,9 @@
inkscape:pagecheckerboard="0"
inkscape:deskcolor="#d1d1d1"
showgrid="true"
inkscape:zoom="0.62608414"
inkscape:cx="566.21782"
inkscape:cy="556.63445"
inkscape:zoom="0.62608415"
inkscape:cx="388.92535"
inkscape:cy="414.48102"
inkscape:window-width="1848"
inkscape:window-height="1016"
inkscape:window-x="72"
......@@ -24520,7 +24520,7 @@
id="page24"
width="1344"
height="960"
inkscape:export-filename="fig1.png"
inkscape:export-filename="fig1.pdf"
inkscape:export-xdpi="96"
inkscape:export-ydpi="96" />
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......@@ -69524,32 +69524,10 @@
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id="g41388" />
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id="g41390">
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xml:space="preserve"
transform="matrix(1,0,0,-1,562.97,368.62)"
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article/figures/fig2.png

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article/figures/fig2.png

232 KB | W: | H:

article/figures/fig2.png
article/figures/fig2.png
article/figures/fig2.png
article/figures/fig2.png
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