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3_CloudPlot_LeafLife.Rmd
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3_CloudPlot_LeafLife.Rmd
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# 1. Load libraries
```{r}
suppressWarnings(suppressMessages(library(ggpubr)))
suppressWarnings(suppressMessages(library(tidyverse)))
suppressWarnings(suppressMessages(library(png)))
suppressWarnings(suppressMessages(library(grid)))
```
# 2. Import data
```{r}
# stats results
result_stats <- read.csv('features_contribution_LeafLife.csv')
# # feature information
result_xcms <- read.csv("../../1_preprocessing/featureDefinitions.csv")
result_xcms <- result_xcms %>% filter(Features %in% result_stats$Features)
#rownames(result_xcms) <- result_xcms$Features
result_xcms <- result_xcms %>% select(Features, rtmed, mzmed)
result_stats <- merge(result_stats, result_xcms, on=0)
```
# CLOUD PLOT FOR `LeafLife`
```{r}
t = 0
# # up-regulated in LIVING
ll.up <- result_stats %>% filter(LL.f.contrib > t) %>% arrange(LL.f.contrib)
# # up-regulated in LIVING
ll.down <- result_stats %>% filter(LL.f.contrib < -t) %>% arrange(desc(LL.f.contrib))
```
# TIC for background
```{r fig.width=8}
# read in for background
img1 <- png::readPNG("tic_Brevideciduous.png")
img2 <- png::readPNG("tic_Deciduous_inv.png")
```
# CLOUD PLOT
```{r}
w=20
h=10
size=15
res=300
t2 = quantile(abs(result_stats$LL.f.contrib), 0.75)
# from GFE listColors <- c('Brevideciduous' = '#AA3377', 'Deciduous' = '#117733')
point.ok.up <- ggplot(ll.up) +
annotation_custom(rasterGrob(img1, width = unit(1,"npc"), height = unit(1,"npc")),
xmin = 0, xmax = 2942, ymin = 10, ymax = 1000) +
geom_point(aes(x = rtmed, y = mzmed, color = LL.f.contrib > t2,
fill = LL.f.contrib > t2, size = LL.f.contrib), alpha=0.5) +
scale_fill_manual(name = 'top contribution ',
values = setNames(c("#AA3377", "antiquewhite3"), c(T, F))) +
scale_color_manual(name = 'top contribution ',
values = setNames(c("#AA3377", "antiquewhite3"), c(T, F))) +
scale_size_continuous(name = 'contribution', range = c(1,8)) +
scale_y_continuous('Features (m/z)', limits = c(0,1000), expand=c(0,0)) +
scale_x_continuous(limits = c(0, 2942), expand=c(0,0)) +
theme_linedraw(base_size = size) +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
legend.text = element_text(size = size, face="bold"),
legend.title = element_text(size = size,face="bold"),
legend.key.size = unit(1, "cm"),
legend.key.width = unit(1,"cm"),
axis.title.y = element_text(size = size,face="bold"),
axis.text.y = element_text(size = size,face="bold"),
panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),) +
guides(colour = guide_legend(override.aes = list(size = 5)))
# point.ok.up
ggsave('cloud_Brevideciduous.png', units=c('in'), width=w, height=h, dpi=res, point.ok.up)
point.ok.down <- ggplot(ll.down) +
annotation_custom(rasterGrob(img2, width = unit(1,"npc"), height = unit(1,"npc")),
xmin = 0, xmax = 2942, ymin = -Inf, ymax = -10) +
geom_point(aes(x = rtmed, y = mzmed, color = LL.f.contrib < -t2,
fill = LL.f.contrib < -t2, size = LL.f.contrib), alpha=0.5) +
scale_fill_manual(name = 'top contribution ',
values = setNames(c("#117733","antiquewhite3"), c(T, F))) +
scale_color_manual(name = 'top contribution ',
values = setNames(c("#117733","antiquewhite3"), c(T, F))) +
scale_size(name = 'contribution', trans="reverse") +
scale_y_reverse('Features (m/z)', limits = c(1000,0), expand=c(0,0)) +
scale_x_continuous(limits = c(0,2942), expand=c(0,0)) +
theme_linedraw(base_size = size) +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
legend.text = element_text(size = size, face="bold"),
legend.title = element_text(size = size,face="bold"),
legend.key.size = unit(1, "cm"),
legend.key.width = unit(1,"cm"),
axis.title.y = element_text(size = size,face="bold"),
axis.text.y = element_text(size = size,face="bold"),
panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),) +
guides(colour = guide_legend(override.aes = list(size = 5)))
# point.ok.down
ggsave('cloud_Deciduous.png', units=c('in'), width=w, height=h, dpi=res, point.ok.down)
cloud <- ggarrange(point.ok.up, point.ok.down, ncol = 1, nrow=2)
# cloud
w=14
h=10
ggsave('CloudPlot__Brevideciduous_vs_Deciduous.png', units=c('in'), width=w, height=h, dpi=res, cloud)
```