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Commit 19f574e2 authored by Xianzong Meng's avatar Xianzong Meng
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Fig beautify

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codes/stasitic.Rmd
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......@@ -220,17 +220,23 @@ anova(ESPND140,ESPND140_sex)
##plot
```{r}
p_SD_foraging <- ggplot(df.SD_Rday1, aes(x=trials, y=foraging.score, group=rat_ID))
SD_Rday1_sum<-df.SD_Rday1 %>% group_by(trials, age) %>% summarize(percentage = sum(foraging.score != 7)/n())
Fig_SD_foraging<- p_SD_foraging +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", aes(group = age, color= age), size = 1, geom = "line", fun.min = 'sd', fun.max = 'sd') +
Fig1a <-ggbarplot(SD_Rday1_sum, x="trials", y="percentage",
color = "age", palette = c("#7fc97f", "#fdc086"),
size = 2, ylab = "foraging success [%]",
position = position_dodge(1))
Fig1b<- ggplot(df.SD_Rday1, aes(x=trials, y=foraging.score, group=rat_ID)) + geom_line(color="gray", alpha=0.2)+
stat_summary(fun=mean, aes(group = age, color= age), geom="line", linewidth=2)+
stat_summary(fun.data = mean_se, aes(group=age, color = age), geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~ age, ncol = 2)
Fig_SD_foraging
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/SD_foraging.svg', plot = Fig_SD_foraging, device = 'svg',dpi = 300)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~age, ncol=2)
Fig1a_1b <- ggarrange(Fig1a, Fig1b, ncols=2,labels=c('A','B'), common.legend=TRUE,legend="right", widths=c(1,2))
Fig1a_1b
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig1a_1b.svg', plot = Fig1a_1b, device = 'svg',dpi = 300, width = 176, height = 140, units = "mm")
```
## SD rat, success rate
......@@ -365,18 +371,23 @@ anova(ESrestriction60,ESrestriction60_sex)
##plot-restriction
```{r}
p_LE_foraging <- ggplot(df.LE_Rday1, aes(x=trials, y=foraging.score, group=rat_ID))
LE_Rday1_sum<-df.LE_Rday1 %>% group_by(trials, restriction) %>% summarize(percentage = sum(foraging.score != 7)/n())
Fig_LE_restriction_foraging <- p_LE_foraging +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", aes(group = restriction, color= restriction), size = 1, geom = "line", fun.min = 'sd', fun.max = 'sd') +
Fig2a <-ggbarplot(LE_Rday1_sum, x="trials", y="percentage",
color = "restriction", palette = c("#beaed4", "#ffff99"),
size = 2, ylab = "foraging success [%]",
position = position_dodge(1))
Fig2b<- ggplot(df.LE_Rday1, aes(x=trials, y=foraging.score, group=rat_ID)) + geom_line(color="gray", alpha=0.2)+
stat_summary(fun=mean, aes(group = restriction, color= restriction), geom="line", linewidth=2)+
stat_summary(fun.data = mean_se, aes(group=restriction, color = restriction), geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#beaed4", "#ffff99"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~restriction, ncol = 2)
Fig_LE_restriction_foraging
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/LE_restriction_foraging.svg', plot = Fig_LE_restriction_foraging, device = 'svg',dpi = 300)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~restriction, ncol=2)
Fig2a_2b <- ggarrange(Fig2a, Fig2b, ncols=2,labels=c('A','B'), common.legend=TRUE,legend="right", widths=c(1,2))
Fig2a_2b
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig2a_2b.svg', plot = Fig2a_2b, device = 'svg',dpi = 300, width = 176, height = 140, units = "mm")
```
##plot_sex effect
#PND70
......@@ -387,9 +398,9 @@ Fig_SD_sex_age_70 <- EFsex_age_70 +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1, aes(group = sex, color= sex), geom = "line", fun.min = 'sd', fun.max = 'sd') +
stat_summary(fun.data = mean_se, geom = "errorbar", aes(group=sex, color = sex), alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#fb9a99", "#a6cee3"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~ sex, ncol = 2)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~ sex, ncol = 2)
Fig_SD_sex_age_70
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_SD_sex_age_70.svg', plot = Fig_SD_sex_age_70, device = 'svg',dpi = 300)
```
......@@ -401,9 +412,9 @@ Fig_SD_sex_age_140 <- EFsex_age_140 +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1,aes(group = sex, color= sex),geom = "line", fun.min = 'sd', fun.max = 'sd') +
stat_summary(fun.data = mean_se,aes(group = sex, color= sex),geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#fb9a99", "#a6cee3"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~ sex, ncol = 2)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~ sex, ncol = 2)
Fig_SD_sex_age_140
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_SD_sex_age_140.svg', plot = Fig_SD_sex_age_140, device = 'svg',dpi = 300)
```
......@@ -415,9 +426,9 @@ Fig_LE_sex_restriction_45 <- EFsex_restriction_45 +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1, aes(group = sex, color= sex),geom = "line", fun.min = 'sd', fun.max = 'sd') +
stat_summary(fun.data = mean_se, aes(group = sex, color= sex),geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#fb9a99", "#a6cee3"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~ sex, ncol = 2)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~ sex, ncol = 2)
Fig_LE_sex_restriction_45
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_LE_sex_restriction_45.svg', plot = Fig_LE_sex_restriction_45, device = 'svg',dpi = 300)
```
......@@ -429,9 +440,9 @@ Fig_LE_sex_restriction_60 <- EFsex_restriction_60 +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1, aes(group = sex, color= sex), geom = "line", fun.min = 'sd', fun.max = 'sd') +
stat_summary(fun.data = mean_se, aes(group = sex, color= sex), geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#fb9a99", "#a6cee3"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~ sex, ncol = 2)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~ sex, ncol = 2)
Fig_LE_sex_restriction_60
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_LE_sex_restriction_60.svg', plot = Fig_LE_sex_restriction_60, device = 'svg',dpi = 300)
```
......@@ -443,9 +454,9 @@ Fig_LE_sex_general <- p_LE_foraging +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1, aes(group = sex, color= sex), geom = "line", fun.min = 'sd', fun.max = 'sd') +
stat_summary(fun.data = mean_se, aes(group = sex, color= sex), geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#fb9a99", "#a6cee3"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~ sex, ncol = 2)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~ sex, ncol = 2)
Fig_LE_sex_general
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_LE_sex_general.svg', plot = Fig_LE_sex_general, device = 'svg',dpi = 300)
```
......@@ -458,9 +469,9 @@ Fig_LE_sex_blineday6_general <- EFsex_blinedays +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1, aes(group = sex, color= sex), geom = "line", fun.min = 'sd', fun.max = 'sd') +
stat_summary(fun.data = mean_se, aes(group = sex, color= sex), geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#fb9a99", "#a6cee3"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "foraging score") + theme_minimal() + facet_wrap(~ sex, ncol = 2)
labs(x = "positions", y = "foraging score") + theme_classic() + facet_wrap(~ sex, ncol = 2)
LE_Bday6 <- lmer(foraging.score~ sex + trials + sex:trials + (1|rat_ID),df.LE_Bday6)
eta_squared(LE_Bday6)
......@@ -468,6 +479,13 @@ eta_squared(LE_Bday6)
Fig_LE_sex_blineday6_general
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_LE_sex_blineday6_general.svg', plot = Fig_LE_sex_blineday6_general, device = 'svg',dpi = 300)
```
## sex effect, ggarange
```{r}
Fig3 <- ggarrange(Fig_SD_sex_age_70,Fig_SD_sex_age_140,Fig_LE_sex_restriction_45,Fig_LE_sex_restriction_60,Fig_LE_sex_general,Fig_LE_sex_blineday6_general,ncol=2, nrow=3,labels=c('A','B','C','D','E','F'),common.legend=TRUE,legend="right")
Fig3
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig3.svg', plot = Fig3, device = 'svg',dpi = 300, width = 176, height = 190, units = "mm")
```
## LE rat, success rate
```{r}
......@@ -524,15 +542,13 @@ eta_squared(mod.score_LE_60_leaving)
```
## leaving figure
```{r}
LE_Rday1_leaving <- ggplot(df.LE_Rday1, aes(x=trials, y=leaving.score, group=rat_ID))
Fig_LE_leaving <- LE_Rday1_leaving +
Fig_LE_leaving <- ggplot(df.LE_Rday1, aes(x=trials, y=leaving.score, group=rat_ID)) +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1, aes(group = restriction, color= restriction), geom = "line", fun.min = 'sd', fun.max = 'sd')+
stat_summary(fun.data = mean_se, aes(group = restriction, color= restriction), geom = "errorbar", alpha=1, width=0.05) +
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#beaed4", "#ffff99"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
labs(x = "positions", y = "leaving score") + theme_minimal() + facet_wrap(~ restriction, ncol = 2)
labs(x = "positions", y = "leaving score") + theme_classic() + facet_wrap(~restriction, ncol = 2)
Fig_LE_leaving
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_LE_leaving.svg', plot = Fig_LE_leaving, device = 'svg',dpi = 300)
```
......@@ -564,18 +580,25 @@ approaching_emm_trials_sex
## approaching figure_restriction
```{r}
LE_Rday1_approaching <- ggplot(df.LE_Rday1, aes(x=trials, y=approaching.score, group=rat_ID))
Fig_LE_approaching <- LE_Rday1_approaching +
Fig_LE_approaching <- ggplot(df.LE_Rday1, aes(x=trials, y=approaching.score, group=rat_ID)) +
geom_line(color="gray", alpha=0.2)+
stat_summary(fun = "mean", size = 1, aes(group = restriction, color= restriction), geom = "line", fun.min = 'sd', fun.max = 'sd')+
stat_summary(fun.data = mean_se, aes(group = restriction, color= restriction), geom = "errorbar", alpha=1, width=0.05)+
scale_color_manual(values = c("#7fc97f", "#fdc086"))+
scale_color_manual(values = c("#beaed4", "#ffff99"))+
scale_y_continuous(breaks = seq(0, 7, by = 1))+
theme_minimal() + facet_wrap(~ restriction, ncol = 2)
theme_classic() + facet_wrap(~ restriction, ncol = 2)
Fig_LE_approaching
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig_LE_approaching.svg', plot = Fig_LE_approaching, device = 'svg',dpi = 300)
```
## Fig4
```{r}
Fig4 <- ggarrange(Fig_LE_leaving, Fig_LE_approaching, ncols=2,labels=c('A','B'), common.legend=TRUE,legend="right")
Fig4
ggsave('C:/Users/xiamen/Desktop/modified robogator/result figs/Fig4.svg', plot = Fig4, device = 'svg',dpi = 300, width = 176, height = 140, units = "mm")
```
## approaching figure_restriction_sex
```{r}
LE_Rday1_approaching <- ggplot(restriction45, aes(x=trials, y=approaching.score, group=rat_ID))
......
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