Commit ab311e94 authored by mariefbourdon's avatar mariefbourdon
Browse files

220704 figures

parent 3ce3a323
No preview for this file type
......@@ -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)
```
......
No preview for this file type
......@@ -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)
```
......
No preview for this file type
No preview for this file type
......@@ -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)
```
......
No preview for this file type
No preview for this file type
......@@ -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)
```
......
No preview for this file type
No preview for this file type
......@@ -24487,6 +24487,13 @@
d="M 0,360 H 504 V 720 H 0 Z"
id="path22112-3" />
</clipPath>
<clipPath
clipPathUnits="userSpaceOnUse"
id="clipPath85256">
<path
d="m 540.72,394.98 h 461.3 v 299.93 h -461.3 z"
id="path85254" />
</clipPath>
</defs>
<sodipodi:namedview
id="namedview20"
......@@ -24498,22 +24505,22 @@
inkscape:pagecheckerboard="0"
inkscape:deskcolor="#d1d1d1"
showgrid="true"
inkscape:zoom="0.44270834"
inkscape:cx="947.57647"
inkscape:cy="964.51764"
inkscape:window-width="1920"
inkscape:window-height="1043"
inkscape:window-x="1920"
inkscape:window-y="0"
inkscape:zoom="0.62608414"
inkscape:cx="566.21782"
inkscape:cy="556.63445"
inkscape:window-width="1848"
inkscape:window-height="1016"
inkscape:window-x="72"
inkscape:window-y="27"
inkscape:window-maximized="1"
inkscape:current-layer="g41414-3">
inkscape:current-layer="g26">
<inkscape:page
x="0"
y="0"
id="page24"
width="1344"
height="960"
inkscape:export-filename="fig1.pdf"
inkscape:export-filename="fig1.png"
inkscape:export-xdpi="96"
inkscape:export-ydpi="96" />
<inkscape:grid
......@@ -69344,161 +69351,6 @@
</g>
<g
id="g41190" />
<g
id="g41192">
<g
id="g41194"
clip-path="url(#clipPath41198)">
<path
d="m 540.72,394.98 h 461.3 v 299.93 h -461.3 z"
style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:none"
id="path41200" />
<path
d="m 567.24,408.62 h 11.34 v 10.49 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41202" />
<path
d="m 578.58,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41204" />
<path
d="m 589.92,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41206" />
<path
d="m 601.25,408.62 h 11.34 v 83.9 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41208" />
<path
d="m 612.59,408.62 h 11.34 v 146.82 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41210" />
<path
d="m 623.93,408.62 h 11.34 v 104.87 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41212" />
<path
d="m 635.27,408.62 h 11.34 v 115.36 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41214" />
<path
d="m 646.6,408.62 h 11.34 V 618.36 H 646.6 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41216" />
<path
d="m 657.94,408.62 h 11.34 v 272.66 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41218" />
<path
d="m 669.28,408.62 h 11.34 v 62.92 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41220" />
<path
d="m 680.62,408.62 h 11.34 v 41.95 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41222" />
<path
d="m 691.95,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41224" />
<path
d="m 703.29,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41226" />
<path
d="m 714.63,408.62 h 11.34 v 0 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41228" />
<path
d="m 725.96,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41230" />
<path
d="m 737.3,408.62 h 11.34 v 52.44 H 737.3 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41232" />
<path
d="m 748.64,408.62 h 11.34 V 503 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41234" />
<path
d="m 759.98,408.62 h 11.34 v 31.46 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41236" />
<path
d="m 771.31,408.62 h 11.34 v 62.92 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41238" />
<path
d="m 782.65,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41240" />
<path
d="m 793.99,408.62 h 11.34 V 503 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41242" />
<path
d="m 805.33,408.62 h 11.34 v 41.95 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41244" />
<path
d="M 816.66,408.62 H 828 v 83.9 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41246" />
<path
d="m 828,408.62 h 11.34 v 62.92 H 828 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41248" />
<path
d="m 839.34,408.62 h 11.34 v 104.87 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41250" />
<path
d="m 850.68,408.62 h 11.34 V 503 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41252" />
<path
d="m 862.01,408.62 h 11.34 v 73.41 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41254" />
<path
d="m 873.35,408.62 h 11.34 v 73.41 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41256" />
<path
d="m 884.69,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41258" />
<path
d="m 896.02,408.62 h 11.34 v 41.95 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41260" />
<path
d="m 907.36,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41262" />
<path
d="m 918.7,408.62 h 11.34 v 62.92 H 918.7 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41264" />
<path
d="m 930.04,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41266" />
<path
d="m 941.37,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41268" />
<path
d="m 952.71,408.62 h 11.34 v 115.36 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41270" />
<path
d="m 964.05,408.62 h 11.34 v 136.33 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path41272" />
</g>
</g>
<g
id="g41274" />
<g
......@@ -72840,5 +72692,165 @@
id="g43876" />
<g
id="g43878" />
<g
id="g85250"
transform="translate(1.3518e-5,2.6737276e-4)">
<g
id="g85252"
clip-path="url(#clipPath85256)">
<path
d="m 540.72,394.98 h 461.3 v 299.93 h -461.3 z"
style="fill:#ffffff;fill-opacity:1;fill-rule:nonzero;stroke:none"
id="path85258" />
<path
d="m 567.24,408.62 h 11.34 v 10.49 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85260" />
<path
d="m 578.58,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85262" />
<path
d="m 589.92,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85264" />
<path
d="m 601.25,408.62 h 11.34 v 83.9 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85266" />
<path
d="m 612.59,408.62 h 11.34 v 146.82 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85268" />
<path
d="m 623.93,408.62 h 11.34 v 104.87 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85270" />
<path
d="m 635.27,408.62 h 11.34 v 115.36 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85272" />
<path
d="m 646.6,408.62 h 11.34 V 618.36 H 646.6 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85274" />
<path
d="m 657.94,408.62 h 11.34 v 272.66 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85276" />
<path
d="m 669.28,408.62 h 11.34 v 62.92 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85278" />
<path
d="m 680.62,408.62 h 11.34 v 41.95 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85280" />
<path
d="m 691.95,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85282" />
<path
d="m 703.29,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85284" />
<path
d="m 714.63,408.62 h 11.34 v 0 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85286" />
<path
d="m 725.96,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85288" />
<path
d="m 737.3,408.62 h 11.34 v 52.44 H 737.3 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85290" />
<path
d="m 748.64,408.62 h 11.34 V 503 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85292" />
<path
d="m 759.98,408.62 h 11.34 v 31.46 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85294" />
<path
d="m 771.31,408.62 h 11.34 v 62.92 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85296" />
<path
d="m 782.65,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85298" />
<path
d="m 793.99,408.62 h 11.34 V 503 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85300" />
<path
d="m 805.33,408.62 h 11.34 v 41.95 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85302" />
<path
d="M 816.66,408.62 H 828 v 83.9 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85304" />
<path
d="m 828,408.62 h 11.34 v 62.92 H 828 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85306" />
<path
d="m 839.34,408.62 h 11.34 v 104.87 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85308" />
<path
d="m 850.68,408.62 h 11.34 V 503 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85310" />
<path
d="m 862.01,408.62 h 11.34 v 73.41 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85312" />
<path
d="m 873.35,408.62 h 11.34 v 73.41 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85314" />
<path
d="m 884.69,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85316" />
<path
d="m 896.02,408.62 h 11.34 v 41.95 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85318" />
<path
d="m 907.36,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85320" />
<path
d="m 918.7,408.62 h 11.34 v 62.92 H 918.7 Z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85322" />
<path
d="m 930.04,408.62 h 11.34 v 20.97 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85324" />
<path
d="m 941.37,408.62 h 11.34 v 52.44 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85326" />
<path
d="m 952.71,408.62 h 11.34 v 115.36 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85328" />
<path
d="m 964.05,408.62 h 11.34 v 136.33 h -11.34 z"
style="fill:#990000;fill-opacity:0.4;fill-rule:nonzero;stroke:none"
id="path85330" />
<path
d="M 720.18,394.98 V 694.91"
style="fill:none;stroke:#000000;stroke-width:1.07;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:10;stroke-dasharray:4.27, 4.27;stroke-dashoffset:0;stroke-opacity:1"
id="path85332" />
</g>
</g>
</g>
</svg>
No preview for this file type
......@@ -16757,7 +16757,7 @@
inkscape:deskcolor="#d1d1d1"
showgrid="false"
inkscape:zoom="0.62608413"
inkscape:cx="262.74424"
inkscape:cx="261.14701"
inkscape:cy="572.60675"
inkscape:window-width="1848"
inkscape:window-height="1016"
......@@ -16771,7 +16771,7 @@
id="page21976"
width="1344"
height="960"
inkscape:export-filename="fig3.pdf"
inkscape:export-filename="fig3.png"
inkscape:export-xdpi="96"
inkscape:export-ydpi="96" />
</sodipodi:namedview>
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment