From 7fc5064a5f9e0c77857fce5b1895277651408c3b Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Wed, 11 Nov 2020 15:29:58 +0100
Subject: [PATCH] Updated figures to R1 - added XW and SbM
---
03_Figures_Simulations.R | 83 +++++++++++++++++++++++++++++++---------
1 file changed, 65 insertions(+), 18 deletions(-)
diff --git a/03_Figures_Simulations.R b/03_Figures_Simulations.R
index 5c19cac..0502cd5 100644
--- a/03_Figures_Simulations.R
+++ b/03_Figures_Simulations.R
@@ -82,11 +82,10 @@ ggplot(data=outp.summary %>%
dplyr::filter(stat.type=="XY") %>%
dplyr::filter(trait %in% c("1", "2", "1 2", "3", "1 3", "2 3")) %>%
mutate(trait=factor(trait, levels=c("1", "2", "3", "1 2", "1 3", "2 3"),
- labels=c("t1", "t2", "tn", "t1 t2", "t1 tn", "t2 tn")))) + #%>%
- #dplyr::filter(trait %in% c("1", "2", "1 2", "3")) %>%
- #mutate(inter=as.factor(inter))) +
- geom_line(aes(x=main, y=power, group=trait, col=trait)) +
- #scale_colour_brewer(palette = "Dark2") +
+ labels=c("t1", "t2", "tn", "t1 t2", "t1 tn", "t2 tn"))) %>%
+ mutate(linetype=as.factor(ifelse(grepl(pattern="tn", x = trait), 2, 1)))) +
+ geom_line(aes(x=main, y=power, group=trait, col=trait, lty=linetype)) +
+ guides(linetype = FALSE) +
scale_color_manual("Trait\ncomb.",
values=c("#e41a1c", #1 - red)
"#e6ab02", #2 - yellow
@@ -102,7 +101,7 @@ ggplot(data=outp.summary %>%
scale_y_continuous(name="Prop. of significant tests") +
theme(panel.grid = element_blank())
-ggsave(filename="_pics/Fig2_CorrInte_02March.png", width=6, height=5, device="png", dpi = 300, last_plot())
+ggsave(filename="_pics/R1/Fig2_CorrInte_02March.png", width=6, height=5, device="png", dpi = 300, last_plot())
@@ -137,7 +136,8 @@ outp.summary2 <- outp.summary %>%
### rename null trait to "tn"
outp.summary2 <- outp.summary2 %>%
mutate(tn.name=paste0("t", ntraits)) %>%
- mutate(trait=str_replace(trait, pattern=tn.name, replacement="tn"))
+ mutate(trait=str_replace(trait, pattern=tn.name, replacement="tn")) %>%
+ mutate(linetype=as.factor(ifelse(grepl(pattern="tn", x = trait), 2, 1)))
#reorder factors
outp.summary2$trait <- factor(outp.summary2$trait, levels= c('t1', 't2','t3', 't4', 'tn',
@@ -167,7 +167,8 @@ outp.summary2 <- outp.summary2 %>%
left_join(hugepalette, by="trait")
fig3 <- ggplot(data=outp.summary2) +
- geom_line(aes(x=main, y=power, group=trait, col=trait.col)) +
+ geom_line(aes(x=main, y=power, group=trait, col=trait.col, lty=linetype)) +
+ guides(linetype = FALSE) +
scale_x_continuous(name="Effect of factor e1 -> trait t1", n.breaks = 4) +
scale_y_continuous(name="Prop. of significant tests") +
facet_grid(sel.ntraits.lab~ntraits.lab) +
@@ -202,7 +203,7 @@ fig3.panel <- cowplot::plot_grid(fig3 + theme(legend.position = "none"),
nrow=1, rel_widths = c(0.6,.4))
-ggsave(filename="_pics/Fig3_TraitNumber.png",
+ggsave(filename="_pics/R1/Fig3_TraitNumber.png",
width=9, height=7, device="png", dpi = 300, fig3.panel)
@@ -221,10 +222,10 @@ ggplot(data=outp.summary %>%
dplyr::filter(stat.type=="XY") %>%
dplyr::filter(trait %in% c("1", "2", "3", "4")) %>%
mutate(trait=factor(trait, levels=c("1", "2", "3", "4"),
- labels=c("t1", "t2", "t3","tn")))) + #%>%
- #dplyr::filter(trait %in% c("1", "2", "1 2", "3")) %>%
- #mutate(inter=as.factor(inter))) +
- geom_line(aes(x=main, y=power, group=trait, col=trait)) +
+ labels=c("t1", "t2", "t3","tn"))) %>%
+ mutate(linetype=as.factor(ifelse(grepl(pattern="tn", x = trait), 2, 1)))) +
+ geom_line(aes(x=main, y=power, group=trait, col=trait, lty=linetype)) +
+ guides(linetype = FALSE) +
#scale_colour_brewer(palette = "Dark2") +
#scale_color_manual("Trait\ncomb.",
scale_color_manual("Trait",
@@ -242,12 +243,14 @@ ggplot(data=outp.summary %>%
scale_y_continuous(name="Prop. of significant tests") +
theme(panel.grid = element_blank())
-ggsave(filename="_pics/FigS4_Extra_CorrInte_08Jul20.png", width=6, height=5, device="png", dpi = 300, last_plot())
+ggsave(filename="_pics/R1/FigS4_Extra_CorrInte_08Jul20.png", width=6, height=5, device="png", dpi = 300, last_plot())
+
+### Additional Figures for JVS R1 ####
-### FIGURE SXXX ####
+#### FIGURE SXXX - XW ####
mypath <- "_data/Experiment_30Oct2020_FactorInteraction&TraitCorr_XW"
myfiles <- list.files(path=mypath, pattern = "Summary.txt", recursive = T)
outp.summary <- FormatData(myfiles)
@@ -267,8 +270,10 @@ ggplot(data=outp.summary %>%
dplyr::filter(stat.type=="XY") %>%
dplyr::filter(trait %in% c("1", "2", "1 2", "3", "1 3", "2 3")) %>%
mutate(trait=factor(trait, levels=c("1", "2", "3", "1 2", "1 3", "2 3"),
- labels=c("t1", "t2", "tn", "t1 t2", "t1 tn", "t2 tn")))) +
- geom_line(aes(x=main, y=power, group=trait, col=trait)) +
+ labels=c("t1", "t2", "tn", "t1 t2", "t1 tn", "t2 tn"))) %>%
+ mutate(linetype=as.factor(ifelse(grepl(pattern="tn", x = trait), 2, 1)))) +
+ geom_line(aes(x=main, y=power, group=trait, col=trait, lty=linetype)) +
+ guides(linetype = FALSE) +
scale_color_manual("Trait\ncomb.",
values=c("#e41a1c", #1 - red)
"#e6ab02", #2 - yellow
@@ -283,9 +288,51 @@ ggplot(data=outp.summary %>%
scale_y_continuous(name="Prop. of significant tests") +
theme(panel.grid = element_blank())
-ggsave(filename="_pics/FigSXXX_CorrInte_30November_XW.png", width=6, height=5, device="png", dpi = 300, last_plot())
+ggsave(filename="_pics/R1/FigSXXX_CorrInte_30November_XW.png", width=6, height=5, device="png", dpi = 300, last_plot())
+
+
+
+
+### FIGURE SXXY - SBM ####
+mypath <- "_data/Experiment_30Oct2020_FactorInteraction&TraitCorr_XW"
+myfiles <- list.files(path=mypath, pattern = "Summary.txt", recursive = T)
+outp.summary <- FormatData(myfiles)
+
+mypalette <- palette(c("#e41a1c", #1 - red)
+ "#ff7f00", #12 - orange
+ "#984ea3", #13 - violet
+ "##ffed6f", #2 - yellow
+ "#4daf4a", #23 - green
+ "#377eb8")) #3 - blue
+ggplot(data=outp.summary %>%
+ mutate(main=main/100) %>%
+ mutate(corr=factor(corr/10, levels=c(0, 0.4, 0.8), labels=paste0("Correlation = ", c(0, 0.4, 0.8)))) %>%
+ mutate(inter=factor(inter/10, levels=c(0, 0.3, 0.5), labels=paste0("Interaction = ", c(0, 0.3, 0.5)))) %>%
+ ungroup() %>%
+ dplyr::filter(stat.type=="SbM") %>%
+ dplyr::filter(envir==1) %>%
+ dplyr::filter(trait %in% c("1", "2", "1 2", "3", "1 3", "2 3")) %>%
+ mutate(trait=factor(trait, levels=c("1", "2", "3", "1 2", "1 3", "2 3"),
+ labels=c("t1", "t2", "tn", "t1 t2", "t1 tn", "t2 tn"))) %>%
+ mutate(linetype=as.factor(ifelse(grepl(pattern="tn", x = trait), 2, 1)))) +
+ geom_line(aes(x=main, y=power, group=trait, col=trait, lty=linetype)) +
+ guides(linetype = FALSE) +
+ scale_color_manual("Trait\ncomb.",
+ values=c("#e41a1c", #1 - red)
+ "#e6ab02", #2 - yellow
+ "#377eb8", #3 - blue
+ "#d95f02", #12 - orange
+ "#984ea3", #13 - violet
+ "#4daf4a" #23 - green
+ )) +
+ facet_grid(corr~inter) +
+ theme_bw() +
+ scale_x_continuous(name="Effect of factor e1 -> trait t1") +
+ scale_y_continuous(name="Prop. of significant tests") +
+ theme(panel.grid = element_blank())
+ggsave(filename="_pics/R1/FigSXXX_CorrInte_30November_SbM.png", width=6, height=5, device="png", dpi = 300, last_plot())
--
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