[email protected] November 11, 2024
library(tidyverse)
library(cowplot)
library(ggpubr)
library(pheatmap)
library(RColorBrewer)
library(vegan)
theme_set(theme_bw())本研究所使用的数据主要来自于两个实验：首先是两个单独培养体系和三个共培养体系在BIOLOG板中含有的71种碳源中的碳源利用情况，其次是三个共培养体系中所含的两个物种的数量。碳源利用情况以A750的吸光值确定，物种数量则由qPCR实验确定。两部分的数据分别保存在“biolog”和“qPCR”数据文件中。
为了方便后续的分析过程,这两部分的数据都经过了必要的预处理，规范了数据格式。
我们首先载入对应数据，查看一下数据的格式。
biolog_24h <- read_csv("data/biolog.csv")
qPCR_data <- read_csv(file="data/qPCR.csv")
head(biolog_24h)
#> # A tibble: 6 × 5
#> ratio0 plate carbon_id A590 A750
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 equal 1 1 0.191 0.138
#> 2 equal 1 2 0.344 0.181
#> 3 equal 1 3 1.37 0.561
#> 4 equal 1 4 1.25 0.778
#> 5 equal 1 5 0.191 0.137
#> 6 equal 1 6 0.259 0.142
head(qPCR_data)
#> # A tibble: 6 × 6
#> ratio0 plate carbon_id EC PP ratio1
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 less 1 10 177416. 175245243. 0.00101
#> 2 less 1 11 239521. 148368132. 0.00161
#> 3 less 1 12 29837437. 142288704. 0.210
#> 4 less 1 13 645563. 162324668. 0.00398
#> 5 less 1 14 52481. 142197847. 0.000369
#> 6 less 1 15 164023932. 156667034. 1.05每一行biolog数据中包含了初始接种比例（ratio0），实验编号（plate），碳源的编号，24h时的碳源利用情况（A750）等信息。
每一行的qPCR数据中包含了初始接种比例（ratio0），实验编号（plate），碳源编号（carbon_id），E.
coli 的定量结果（EC），P. putida
的定量结果（PP），以及最终的物种比例（ratio1）。
最后，读取碳源的名称。
carbon_name <- read_csv("data/carbon.csv")
head(carbon_name)
#> # A tibble: 6 × 2
#> carbon_id carbon_source
#> <dbl> <chr>
#> 1 2 Dextrin
#> 2 3 D-Maltose
#> 3 4 D-Trehalose
#> 4 5 D-Cellobiose
#> 5 6 Gentiobiosse
#> 6 7 SucroseqPCR_data <- qPCR_data %>%
mutate(ratio0 = factor(ratio0, levels = c("less","equal","more")))
# Normalization
biolog_24h <- biolog_24h %>%
mutate(ratio0 = factor(ratio0, levels = c("none","less","equal","more","all"))) %>%
group_by(plate,ratio0) %>%
mutate(A590=A590-A590[carbon_id==1],A750=A750-A750[carbon_id==1]) %>%
filter(carbon_id!=1) %>%
ungroup()
biolog_mono_24h <- biolog_24h %>%
filter(ratio0 %in% c("none","all")) %>%
mutate(species=factor(ratio0,levels = c("all","none"),labels = c("E. coli","P. putida"))) %>%
select(-ratio0)
biolog_coculture_24h <- biolog_24h %>%
filter(ratio0 %in% c("less","equal","more")) %>%
mutate(ratio0 = factor(ratio0, levels = c("less","equal","more")))定义碳源利用的分组：U1，U2，U3。分组采用了层级聚类方法，将碳源分为三类。参见 @ref(table1)。
M_A750_24h <- biolog_24h %>% mutate(sample=paste(ratio0,plate,sep="-")) %>%
select(sample,carbon_id,A750) %>%
spread(key=sample,value=A750) %>%
as.data.frame() %>%
tibble::column_to_rownames(var="carbon_id")
k3 <- cutree(hclust(dist(M_A750_24h)),k=3)
carbon_group <- data.frame(usage=k3) %>%
rownames_to_column(var="carbon_id") %>%
mutate(carbon_id=as.numeric(carbon_id)) %>%
mutate(usage=paste("U",usage,sep=""))根据 E. coli 和 P.putida 在单独培养时利用碳源能力的差异，将碳源又分为 E. coli 偏好性碳源、 P. putida 偏好性碳源及其它碳源。参见 @ref(table1)。
biolog_mono_A750_24h <- biolog_mono_24h %>%
select(plate,carbon_id,species,A750) %>%
spread(species,A750)
PP_prefered <- biolog_mono_A750_24h %>%
group_by(carbon_id) %>%
summarise(p=t.test(`P. putida`,`E. coli`,alternative = "greater")$p.value) %>%
filter(p<0.05)
EC_prefered <- biolog_mono_A750_24h %>%
group_by(carbon_id) %>%
summarise(p=t.test(`P. putida`,`E. coli`,alternative = "less")$p.value) %>%
filter(p<0.05)
carbon_prefer <- data.frame("carbon_id"=carbon_name$carbon_id,
"prefer"="none",
stringsAsFactors = F)
carbon_prefer[carbon_prefer$carbon_id %in% EC_prefered$carbon_id,"prefer"] <- "EC"
carbon_prefer[carbon_prefer$carbon_id %in% PP_prefered$carbon_id,"prefer"] <- "PP"相互作用通常被认为是物种间的固有属性。负的相互作用可能来自于底物竞争、抗生素的合成等，而正的相互作用可能来自于代谢的耦联等。
对于共培养体系而言，其总的碳源利用效率与其中包括的两个物种的碳源利用能力和它们在体系中所占的比例相关。在最简单的情况下，如果总的碳源利用效率高于单独培养时最大的碳源利用效率，那么显然是正的相互作用；如果总的碳源利用效率低于单独培养时最小的碳源利用效率，那么则显然是负的相互作用。但是，实际上共培养体系的碳源利用效率较少出现这两种情况，而多介于最大和最小之间，这时就需要综合考虑两个物种所占有的比例。基于这一思考，我们提出了下列理论模型。
Table 1 包括了实验中的71中碳源的编号、名称，及按照前述分类指标的分类情况。
library(kableExtra)
left_join(carbon_name,carbon_group) %>%
left_join(carbon_prefer) %>%
kable()|
carbon_id |
carbon_source |
usage |
prefer |
|---|---|---|---|
|
2 |
Dextrin |
U1 |
none |
|
3 |
D-Maltose |
U2 |
EC |
|
4 |
D-Trehalose |
U2 |
EC |
|
5 |
D-Cellobiose |
U1 |
none |
|
6 |
Gentiobiosse |
U1 |
none |
|
7 |
Sucrose |
U1 |
none |
|
8 |
D-Turanose |
U1 |
none |
|
9 |
Stachyose |
U1 |
none |
|
10 |
D-Raffinose |
U1 |
none |
|
11 |
α-D-Lactose |
U1 |
none |
|
12 |
D-Melibiose |
U1 |
EC |
|
13 |
β-Methyl-D-Glucoside |
U1 |
none |
|
14 |
D-Salicin |
U1 |
none |
|
15 |
N-Acetyl-D-Glucosamine |
U2 |
none |
|
16 |
N-Acetyl-β-Dmannosamine |
U1 |
none |
|
17 |
N-Acetyl-D-Galactosamine |
U1 |
none |
|
18 |
N-AcetylNeuraminic Acid |
U2 |
none |
|
19 |
α-D-Glucose |
U3 |
PP |
|
20 |
D-Mannose |
U3 |
PP |
|
21 |
D-Fructose |
U2 |
EC |
|
22 |
D-Galactose |
U1 |
none |
|
23 |
3-MethylGlucose |
U1 |
none |
|
24 |
D-Fucose |
U1 |
none |
|
25 |
L-Fucose |
U2 |
none |
|
26 |
L-Rhamnose |
U1 |
none |
|
27 |
Inosine |
U2 |
none |
|
28 |
D-Sorbitol |
U1 |
EC |
|
29 |
D-Mannitol |
U2 |
EC |
|
30 |
D-Arabitol |
U1 |
none |
|
31 |
myo-Inositol |
U1 |
none |
|
32 |
Glycerol |
U1 |
PP |
|
33 |
D-Glucose-6-PO4 |
U1 |
EC |
|
34 |
D-Fructose-6-PO4 |
U1 |
EC |
|
35 |
D-Aspartic Acid |
U1 |
none |
|
36 |
D-Serine |
U2 |
none |
|
37 |
Gelatin |
U1 |
none |
|
38 |
Glycyl-L-Prolin |
U1 |
none |
|
39 |
L-Alanine |
U3 |
PP |
|
40 |
L-Arginine |
U1 |
PP |
|
41 |
L-Aspartic Acid |
U3 |
PP |
|
42 |
L-Glutamic |
U3 |
PP |
|
43 |
L-Histidine |
U3 |
PP |
|
44 |
L-Pyroglutamic |
U3 |
PP |
|
45 |
L-Serine |
U1 |
none |
|
46 |
Pectin |
U1 |
EC |
|
47 |
D-Galacturonic Acid |
U3 |
PP |
|
48 |
L-Galactonic Acid Lactone |
U1 |
none |
|
49 |
D-Gluconic |
U3 |
PP |
|
50 |
D-Glucuronic |
U3 |
PP |
|
51 |
Glucuronamid |
U1 |
none |
|
52 |
Mucic Acid |
U3 |
PP |
|
53 |
Quinic Acid |
U3 |
PP |
|
54 |
D-Saccharic |
U3 |
none |
|
55 |
p-Hydroxy-Phenylacetic Acid |
U1 |
none |
|
56 |
Methyl Pyruvate |
U1 |
PP |
|
57 |
D-Lactic Acid Methyl Ester |
U1 |
none |
|
58 |
L-Lactic Acid |
U3 |
PP |
|
59 |
Citric Acid |
U3 |
PP |
|
60 |
α-Keto-Glutaric Acid |
U1 |
PP |
|
61 |
D-Malic Acid |
U1 |
none |
|
62 |
L-Malic Acid |
U3 |
PP |
|
63 |
Bromo-Succinic |
U1 |
PP |
|
64 |
Tween 40 |
U1 |
none |
|
65 |
y-Amino-ButryricAcid |
U3 |
PP |
|
66 |
α-Hydroxy-ButyricAcid |
U1 |
none |
|
67 |
β-Hydroxy-D,L-ButyricAcid |
U1 |
PP |
|
68 |
α-Keto-ButyricAcid |
U1 |
none |
|
69 |
Acetoacetic Acid |
U1 |
PP |
|
70 |
Propionic Acid |
U1 |
PP |
|
71 |
Acetic Acid |
U1 |
none |
|
72 |
Formic Acid |
U1 |
none |
Figure 2 主要展示了共培养体系中最终比例的差异。最终比例以 E. coli 与 P. putida 定量结果的比值为依据。采用 ANOVA 分析三个共培养体系的最终比例是否有差异。P值使用 “BH” 方法做矫正。
aov_p <- compare_means(ratio1~ratio0,
group.by = "carbon_id",
data=qPCR_data,
method = "anova",
p.adjust.method = "BH") %>%
arrange(p.adj)为了展示结果，针对于存在显著差异和不存在显著差异的结果，分别选择了5个典型作为示例。
carbon_name_labeller <- function(x){
name_of <- carbon_name$carbon_source
names(name_of) <- carbon_name$carbon_id
return(as.character(name_of[x]))
}
selected_significant_carbon_id <- c(29,32,36,39,46)
selected_nonsignificant_carbon_id <- c(3,4,7,19,45)
p1 <- ggplot(
data=filter(qPCR_data,carbon_id %in% selected_significant_carbon_id) %>%
left_join(aov_p),
mapping = aes(ratio0,ratio1))
p2 <- ggplot(
data=filter(qPCR_data,carbon_id %in% selected_nonsignificant_carbon_id) %>%
left_join(aov_p),
mapping = aes(ratio0,ratio1))
plots <- lapply(list(p1,p2),function(x){
x + geom_boxplot() + geom_jitter() +
geom_text(aes(x="equal", y=0.55,label= paste("p.adj = ",p.adj)),check_overlap = T) +
geom_text(aes(x="less",y=.65,label=carbon_id),color="grey",size=3) +
facet_wrap(~carbon_id,
ncol=5,
labeller = labeller(carbon_id=carbon_name_labeller)) +
# stat_compare_means(method="aov") +
labs(x="",y="final ratio (EC/PP)")
})
plot_grid(plotlist = plots,ncol=1,labels="AUTO")
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <ce>
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <b1>
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <ce>
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <b1>
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <ce>
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <b1>
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <ce>
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : conversion failure on 'α-D-Glucose' in 'mbcsToSbcs': dot
#> substituted for <b1>
同时，在子图中展示了P值的分布情况。
p.cutoff <- 0.05
p1 <- ggplot(aov_p,aes(p.adj)) +
# geom_histogram(bins=30) +
geom_line(stat = "density",lwd=1) +
geom_density(lwd=0,color=NA,fill="lightblue") +
geom_vline(xintercept = p.cutoff,lwd=1,lty="dashed",color="firebrick") +
geom_text(x=0.06,y=0,label=p.cutoff,
vjust="top",
hjust="left",
color="firebrick")
aov_p$p.adj.signif <- cut(aov_p$p.adj,breaks = c(0,0.01,0.05,1),labels = c("**","*","ns"))
freq <- as.data.frame(table(aov_p$p.adj.signif))
p2 <- ggplot(freq,aes(Var1,Freq)) + geom_col() +
labs(x="significance of p.adj",y="frequency") +
geom_text(aes(label=Freq),vjust=0,nudge_y = 1) +
ylim(c(0,50))
library(grid)
vp <- viewport(width=0.4,height=0.6,x=0.7,y=0.6)
pushViewport(vp)
p1
print(p2,vp=vp)
与@ref(fig2) 对应，Figure S2展示了全部共培养体系的最终比例差异。
ggplot(qPCR_data,aes(ratio0,ratio1)) + geom_boxplot() +
geom_text(aes(x="equal",y=.001,label=carbon_id),color="grey",vjust=1,size=3,show.legend = F) +
# ggpubr::stat_compare_means(method="aov",label="p.signif") +
facet_wrap(~carbon_id) +
# geom_jitter() +
geom_text(aes(x="equal", y=1,label= p.adj),check_overlap = T, data=aov_p) +
# scale_y_log10(breaks=c(0.001,0.01,0.1,1,10),labels=c("0.001","0.01","0.1","1","10")) +
xlab("") + ylab("final ratio (EC/PP)") +
theme(axis.text.x = element_text(angle = 90,hjust = 1,vjust = 0.5),
legend.position = "top",
legend.direction = "horizontal",
strip.background = element_blank(), # remove facet label - "strip"
strip.text = element_blank())
Figure 3展示了碳源偏好性对共培养体系最终比例的影响。
这个影响可以从两个方面来看，一是对于一个确定初始比例的共培养体系，由于碳源偏好性的差异，可以得到：在E. coli偏好性的碳源中生长有利于提高最终比例；在 P. putida 偏好性的碳源中生长则有利于降低最终比例。
另一方面，是在碳源确定的情况下，我们发现，在 E. coli 偏好性的碳源中，初始比例差异较大的三个共培养体系的最终比例趋于一致。其总体上差异已经不再显著。而在其它类型碳源中则没有观察到这一现象。
p <- left_join(biolog_mono_24h,carbon_prefer) %>%
filter(prefer!="none") %>%
ggplot(aes(factor(carbon_id),A750,color=species)) +
geom_boxplot() +
facet_wrap(~prefer,scales="free_y",ncol=1) +
labs(y="CUE",x="carbon id")+
coord_flip() +
theme(legend.position = c(0.8,0.2),
legend.text = element_text(face = "italic"))
library(grid)
library(gtable)
# adjust panel height
gp <- ggplotGrob(p)
# gtable_show_layout(gp)
facet.rows <- gp$layout$t[grepl("panel",gp$layout$name)]
y.var <- sapply(ggplot_build(p)$layout$panel_scales_x,
function(l) length(l$range$range))
gp$heights[facet.rows] <- gp$heights[facet.rows] * y.varp1 <- left_join(qPCR_data,carbon_prefer) %>% ggplot(aes(x=prefer,y=ratio1)) +
geom_boxplot() +
facet_wrap(~ratio0) +
stat_compare_means(method="wilcox.test",comparisons = list(c("EC","none"),c("none","PP"),c("EC","PP"))) +
labs(x="type of carbon perference", y="final ratio (EC/PP)") +
ylim(c(NA,1.5))
p2 <- left_join(qPCR_data,carbon_prefer) %>% ggplot(aes(x=ratio0,y=ratio1)) +
geom_boxplot() +
facet_wrap(~prefer) +
stat_compare_means(method="wilcox.test",comparisons = list(c("less","equal"),c("equal","more"),c("less","more"))) +
labs(x="inital ratio (EC/PP)", y="final ratio (EC/PP)") +
ylim(c(NA,1.5))plot_grid(gp,plot_grid(p1,p2,labels = c("B","C"),ncol = 2),labels = c("A",""),ncol = 1,rel_heights = c(1.5,1))
在接下来的分析中，我们把三个共培养体系视为一个简单的合成群落，通过分析群落对71种碳源的利用能力比较群落功能的差异。
首先，我们分析3个共培养体系CUE的数值分布是不同的。中位数的比较可以窥其一斑。PCA的结果则明确指出了“equal”和“more”的共培养体系具有与单独培养体系和“less”共培养体系完全不同的CUE谱。这一结果在热图中进一步得到体现。
由此，我们可以发现，U2类的碳源在“equal”和“more”中的利用效率显著提高。而在“less”中没有这种现象。说明初始比例的差异最终能够导致群落功能上走向不同的终点。
p_cue <- ggplot(biolog_24h,aes(ratio0,A750)) +
geom_boxplot() +
# stat_compare_means(ref.group = ".all.",
# label = "p.format",
# method="wilcox.test") +
geom_hline(aes(yintercept = median(A750)),lty=2,color="firebrick") +
geom_text(aes(ratio0,y,label=y),
inherit.aes = F,
# color="firebrick",
data = biolog_24h %>% group_by(ratio0) %>%
summarise(y=median(A750)),
vjust=-0.3) +
labs(x="initial ratio (EC/PP)",y="CUE")# 定义一个在PCA图中绘制置信区间的函数
add_ellipase <- function(p, x="PC1", y="PC2", group="group",
ellipase_pro = 0.95,
linetype="dashed",
colour = "black",
lwd = 1,...){
obs <- p$data[,c(x, y, group)]
colnames(obs) <- c("x", "y", "group")
ellipse_pro <- ellipase_pro
theta <- c(seq(-pi, pi, length = 50), seq(pi, -pi, length = 50))
circle <- cbind(cos(theta), sin(theta))
ell <- plyr::ddply(obs, 'group', function(x) {
if(nrow(x) <= 2) {
return(NULL)
}
sigma <- var(cbind(x$x, x$y))
mu <- c(mean(x$x), mean(x$y))
ed <- sqrt(qchisq(ellipse_pro, df = 2))
data.frame(sweep(circle %*% chol(sigma) * ed, 2, mu, FUN = '+'))
})
names(ell)[2:3] <- c('x', 'y')
ell <- plyr::ddply(ell, plyr::.(group) , function(x) x[chull(x$x, x$y), ])
p <- p + geom_polygon(data = ell,
aes(x=x,y=y,group = group),
colour = colour,
linetype=linetype,
lwd =lwd,
inherit.aes = F,
...)
return(p)
}library(vegan)
pca <- rda(t(M_A750_24h))
percent_var <- pca$CA$eig/pca$tot.chi
df <- scores(pca)$sites %>%
as.data.frame() %>%
tibble::rownames_to_column(var="sample") %>%
separate(sample,c("ratio0","rep"),sep="-",remove = F)
df$ratio0 <- factor(df$ratio0, levels = c("none","less","equal","more","all"))
group <- cutree(hclust(dist(t(M_A750_24h))),k=3)
clustered_group <- as.data.frame(group) %>% tibble::rownames_to_column(var = "sample")
df %<>% left_join(clustered_group)
p <- ggplot(df, aes(PC1,PC2,label=ratio0,color=ratio0))+
geom_point(size=3,show.legend = F) +
scale_color_manual(values = brewer.pal(9,"YlOrRd")[5:9],name="Initial Ratio")+
xlab(paste0("PC1: ", round(percent_var[1] * 100), "% variance")) +
ylab(paste0("PC2: ", round(percent_var[2] * 100), "% variance")) +
directlabels::geom_dl(method="smart.grid",size=3)
p_pca <- add_ellipase(p,alpha=0.1,show.legend = F,lwd=1)anno_carbon_group <- carbon_group %>%
left_join(carbon_prefer) %>%
column_to_rownames(var="carbon_id")
p_heatmap <- pheatmap(t(M_A750_24h),
annotation_col = anno_carbon_group[c(2,1)],
cutree_cols = 3,
# cutree_rows = 3,
fontsize_col = 6,
silent = T)plot_grid(plot_grid(p_cue,p_pca,ncol = 2,labels = c("A","B")),
ggplotify::as.ggplot(p_heatmap),ncol = 1,labels = c("","C"),
rel_heights = c(0.8,1))
由于U2类碳源表现了独特现象。我们列出U2类碳源中的CUE和最终比例。
biolog_24h_U2 <- left_join(biolog_24h,carbon_group) %>% filter(usage=="U2")
hsd_group <- lapply(unique(biolog_24h_U2$carbon_id), function(x){
m <- aov(A750~ratio0,data=filter(biolog_24h_U2,carbon_id==x))
library(agricolae)
g <- HSD.test(m,"ratio0",group=TRUE)$groups
d <- rownames_to_column(g,var="ratio0")
d$carbon_id <- x
return(d[-2])
})
hsd_group <- do.call("rbind",hsd_group)
hsd_group$ratio0 <- factor(hsd_group$ratio0,
levels = c("none","less","equal","more","all"))
# add group on top of boxplot
hsd_group <- biolog_24h_U2 %>% group_by(ratio0,carbon_id) %>% summarize(q3=quantile(A750)[3]) %>% left_join(hsd_group)u2_p1 <- ggplot(biolog_24h_U2, aes(ratio0,A750)) +
geom_boxplot() +
geom_text(aes(x="none",y=max(A750)*1.1,label=carbon_id),color="grey",vjust=1,size=3,show.legend = F) +
geom_text(aes(x=ratio0,y=q3,label=groups),show.legend = F,
data = hsd_group,inherit.aes = F,
vjust=0,nudge_y = .2,hjust=0) +
facet_wrap(~carbon_id,ncol=3,
labeller = labeller(carbon_id=carbon_name_labeller)) +
scale_y_continuous(breaks = c(0,0.5,1)) +
labs(x="",y="CUE") +
# ggpubr::stat_compare_means(method="aov",label="p.format") +
theme(axis.text.x = element_text(angle = 45,hjust = 1,vjust = 1),
legend.position = "top",
legend.direction = "horizontal"
)u2_p2 <- left_join(qPCR_data,carbon_group) %>%
left_join(aov_p) %>%
filter(usage=="U2") %>%
ggplot(aes(ratio0,ratio1)) +
geom_boxplot() +
facet_wrap(~carbon_id) +
# geom_jitter() +
geom_text(aes(x="equal", y=1,label= paste("p.adj = ",p.adj)),check_overlap = T) +
geom_text(aes(x="less",y=1,label=carbon_id),color="grey",size=3,hjust=1,vjust=1,nudge_x = -0.1,nudge_y = 0.1) +
facet_wrap(~carbon_id,
ncol=3,
labeller = labeller(carbon_id=carbon_name_labeller)) +
# stat_compare_means(method="aov") +
labs(x="",y="final ratio (EC/PP)") +
# scale_y_log10(breaks=c(0.001,0.01,0.1,1,10),labels=c("0.001","0.01","0.1","1","10")) +
theme(axis.text.x = element_text(angle = 45,hjust = 1,vjust = 1) )plot_grid(u2_p1,u2_p2,labels = "AUTO",ncol=1)
与@ref(fig:fig5) 对应，Figure S3展示了所有的CUE利用情况及差异。
ggplot(biolog_24h, aes(ratio0,A750)) +
geom_boxplot() +
geom_text(aes(x="less",y=max(A750)*1.1,label=carbon_id),
color="grey",
vjust=1,size=3,show.legend = F) +
facet_wrap(~carbon_id,ncol=9) +
scale_y_continuous(breaks = c(0,0.5,1),name = "CUE") +
theme(axis.text.x = element_text(angle = 90,hjust = 1,vjust = 0.5),
legend.position = "top",
legend.direction = "horizontal",
strip.background = element_blank(), # remove facet label - "strip"
strip.text = element_blank())
定义相互作用的类型。首先，根据 monoculture 的 CUE 和 coculture 中的物种比例，计算理论值。然后，拿理论CUE值与实际测得的值进行比较，从而确定相互作用类型。
ratio1 <- qPCR_data %>% filter(ratio0 %in% c("less","equal","more")) %>%
complete(ratio0,carbon_id,plate) %>%
group_by(ratio0,carbon_id) %>%
select(ratio0,plate,carbon_id,ratio1) %>%
mutate(ratio1_mean=mean(ratio1,na.rm = T)) %>%
mutate(ratio1=ifelse(is.na(ratio1),ratio1_mean,ratio1)) %>%
select(-ratio1_mean)
mono_A750 <- biolog_mono_24h %>%
group_by(carbon_id,species) %>%
summarise(A750=mean(A750)) %>%
spread(key="species",value="A750")
A750_caculated <- left_join(ratio1,mono_A750) %>% mutate(A750_cac=(`P. putida`+ratio1*`E. coli`)/(1+ratio1))
social <- biolog_coculture_24h %>% select(plate,carbon_id,ratio0,A750) %>%
left_join(A750_caculated) %>%
group_by(carbon_id,ratio0) %>%
summarise(p_pos=t.test(x=A750,y=A750_cac,alternative = "greater")$p.value,
p_neg=t.test(x=A750,y=A750_cac,alternative = "less")$p.value)
# social$p_pos.adj <- p.adjust(social$p_pos,method = "BH")
# social$p_neg.adj <- p.adjust(social$p_neg,method = "BH")
# 没有同时显著的情况
# any(social$p_neg.adj < 0.05 & social$p_pos.adj < 0.05)
social <- social %>%
mutate(social_type=ifelse(
p_pos<0.05,"+",
ifelse(p_neg<0.05,"-","unresolved"))
) %>%
ungroup() %>%
mutate(ratio0=factor(ratio0,levels = c("less","equal","more")))
biolog_with_social <- biolog_coculture_24h %>% left_join(social)carbon_group <- left_join(carbon_group,carbon_prefer)# social vs ratio0
plots <- lapply(list(c("ratio0","social_type"),c("ratio0","usage","social_type"),c("ratio0","prefer","social_type")), function(x){
df <- social %>% left_join(carbon_group,by="carbon_id") %>%
group_by(.dots=x) %>%
summarise(count=n()) %>%
mutate(proportion=count/sum(count)) %>%
mutate(label=paste(round(proportion*100),"%",sep=""))
ggplot(df,aes_string("ratio0","proportion",fill="social_type")) +
geom_col() +
geom_text(aes(label=label),color="white",
position = position_stack(vjust=0.5),
size=3) +
scale_fill_manual(values = c("+"="firebrick","-"="royalblue","unresolved"="grey"),
name="effect of mixing") +
theme(legend.position = "none",
legend.title = element_text(face="bold")) +
xlab("")
})
#> Warning: The `.dots` argument of `group_by()` is deprecated as of dplyr 1.0.0.
#> ℹ The deprecated feature was likely used in the dplyr package.
#> Please report the issue at <https://github.com/tidyverse/dplyr/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
legend <- get_legend(plots[[1]] + theme(legend.position = c(0.5,0.7)))blank <- ggplot()+theme_void()
plot_grid(plot_grid(blank, plots[[1]], legend, rel_widths = c(0.3,0.8,0.7),ncol=3),
plots[[2]] + facet_wrap(~usage ),
plots[[3]] + facet_wrap(~prefer),
ncol=1,
labels = c("AUTO"))
Figure S4 与 Figure 6 对应，展示所有组合中的相互作用类型。
ggplot(biolog_with_social,aes(ratio0,A750,color=social_type)) +
geom_boxplot() +
geom_text(aes(x="less",y=max(A750)*1.1,label=carbon_id),vjust=1,color="grey",size=3) +
facet_wrap(~carbon_id,ncol=9) +
scale_color_manual(values=c("+"="firebrick","-"="royalblue","unresolved"="grey"),
name="effect of mixing: ") +
scale_y_continuous(breaks = c(0,0.5,1)) +
labs(x="",y="CUE") +
theme(axis.text.x = element_text(angle = 90,hjust = 1,vjust = 0.5),
legend.position = "top",
strip.background = element_blank(), # remove facet label - "strip"
strip.text = element_blank())