R语言可视化学习笔记之添加p-value和显著性标记
http://www.jianshu.com/p/b7274afff14f?from=timeline
上篇文章中提了一下如何通过ggpubr包为ggplot
图添加p-value
以及显著性标记,本文将详细介绍。利用数据集ToothGrowth进行演示
#先加载包 library(ggpubr) #加载数据集ToothGrowth data("ToothGrowth") head(ToothGrowth)
## len supp dose ## 1 4.2 VC 0.5 ## 2 11.5 VC 0.5 ## 3 7.3 VC 0.5 ## 4 5.8 VC 0.5 ## 5 6.4 VC 0.5 ## 6 10.0 VC 0.5
比较方法
R中常用的比较方法主要有下面几种:
方法 | R函数 | 描述 |
---|---|---|
T-test | t.test() | 比较两组(参数) |
Wilcoxon test | wilcox.test() | 比较两组(非参数) |
ANOVA | aov()或anova() | 比较多组(参数) |
Kruskal-Wallis | kruskal.test() | 比较多组(非参数) |
各种比较方法后续有时间一一讲解。
添加p-value
主要利用ggpubr包中的两个函数:
compare_means()
:可以进行一组或多组间的比较stat_compare_mean()
:自动添加p-value
、显著性标记到ggplot图中
compare_means()函数
该函数主要用用法如下:
compare_means(formula, data, method = "wilcox.test", paired = FALSE, group.by = NULL, ref.group = NULL, ...)
注释:
formula
:形如x~group
,其中x是数值型变量,group
是因子,可以是一个或者多个data
:数据集method
:比较的方法,默认为"wilcox.test"
, 其他可选方法为:"t.test"
、"anova"
、"kruskal.test"
paired
:是否要进行paired test
(TRUE
orFALSE
)group_by
: 比较时是否要进行分组ref.group
: 是否需要指定参考组
stat_compare_means()函数
主要用法:
stat_compare_means(mapping = NULL, comparisons = NULL hide.ns = FALSE, label = NULL, label.x = NULL, label.y = NULL, ...)
注释:
mapping
:由aes()
创建的一套美学映射comparisons
:指定需要进行比较以及添加p-value
、显著性标记的组hide.ns
:是否要显示显著性标记nslabel
:显著性标记的类型,可选项为:p.signif
(显著性标记)、p.format
(显示p-value
)label.x
、label.y
:显著性标签调整- ...:其他参数
比较独立的两组
compare_means(len~supp, data=ToothGrowth)
结果解释:
.y
:测试中使用的y变量p
:p-value
p.adj
:调整后的p-value
。默认为p.adjust.method="holm"
p.format
:四舍五入后的p-value
p.signif
:显著性水平method
:用于统计检验的方法绘制箱线图
p <- ggboxplot(ToothGrowth, x="supp", y="len", color = "supp", palette = "jco", add = "jitter")#添加p-valuep+stat_compare_means()
#使用其他统计检验方法 p+stat_compare_means(method = "t.test")
上述显著性标记可以通过label.x
、label.y
、hjust
及vjust
来调整
显著性标记可以通过aes()
映射来更改:aes(label=..p.format..)
或aes(lebel=paste0("p=",..p.format..))
:只显示p-value
,不显示统计检验方法aes(label=..p.signif..)
:仅显示显著性水平aes(label=paste0(..method..,"\n", "p=",..p.format..))
:p-value
与显著性水平分行显示
举个栗子:
p+stat_compare_means(aes(label=..p.signif..), label.x = 1.5, label.y = 40)
也可以将标签指定为字符向量,不要映射,只需将p.signif两端的..去掉即可
p+stat_compare_means(label = "p.signif", label.x = 1.5, label.y = 40)
比较两个paired sample
compare_means(len~supp, data=ToothGrowth, paired = TRUE)
利用ggpaired()进行可视化
ggpaired(ToothGrowth, x="supp", y="len", color = "supp", line.color = "gray", line.size = 0.4, palette = "jco")+ stat_compare_means(paired = TRUE)
多组比较
Global test
compare_means(len~dose, data=ToothGrowth, method = "anova")
可视化
ggboxplot(ToothGrowth, x="dose", y="len", color = "dose", palette = "jco")+ stat_compare_means()
#使用其他的方法 ggboxplot(ToothGrowth, x="dose", y="len", color = "dose", palette = "jco")+ stat_compare_means(method = "anova")
Pairwise comparisons:如果分组变量中包含两个以上的水平,那么会自动进行pairwise test,默认方法为"wilcox.test"
compare_means(len~dose, data=ToothGrowth)
#可以指定比较哪些组 my_comparisons <- list(c("0.5", "1"), c("1", "2"), c("0.5", "2")) ggboxplot(ToothGrowth, x="dose", y="len", color = "dose",palette = "jco")+ stat_compare_means(comparisons=my_comparisons)+ # Add pairwise comparisons p-value stat_compare_means(label.y = 50) # Add global p-value
可以通过修改参数label.y来更改标签的位置
ggboxplot(ToothGrowth, x="dose", y="len", color = "dose",palette = "jco")+ stat_compare_means(comparisons=my_comparisons, label.y = c(29, 35, 40))+ # Add pairwise comparisons p-value stat_compare_means(label.y = 45) # Add global p-value
至于通过添加线条来连接比较的两组,这一功能已由包ggsignif实现
##设定参考组 compare_means(len~dose, data=ToothGrowth, ref.group = "0.5", #以dose=0.5组为参考组 method = "t.test" )
#可视化 ggboxplot(ToothGrowth, x="dose", y="len", color = "dose", palette = "jco")+ stat_compare_means(method = "anova", label.y = 40)+ # Add global p-value stat_compare_means(label = "p.signif", method = "t.test", ref.group = "0.5") # Pairwise comparison against reference
参考组也可以设置为.all.即所有的平均值
compare_means(len~dose, data=ToothGrowth, ref.group = ".all.", method = "t.test")
#可视化 ggboxplot(ToothGrowth, x="dose", y="len", color = "dose", palette = "jco")+ stat_compare_means(method = "anova", label.y = 40)+# Add global p-value stat_compare_means(label = "p.signif", method = "t.test", ref.group = ".all.")#Pairwise comparison against all
接下来利用survminer包中的数据集myeloma来讲解一下为什么有时候我们需要将ref.group设置为.all.
library(survminer)#没安装的先安装再加载 data("myeloma") head(myeloma)
我们将根据患者的分组来绘制DEPDC1基因的表达谱,看不同组之间是否存在显著性的差异,我们可以在7组之间进行比较,但是这样的话组间比较的组合就太多了,因此我们可以将7组中每一组与全部平均值进行比较,看看DEPDC1基因在不同的组中是否过表达还是低表达。
compare_means(DEPDC1~molecular_group, data = myeloma, ref.group = ".all.", method = "t.test")
#可视化DEPDC1基因表达谱 ggboxplot(myeloma, x="molecular_group", y="DEPDC1", color = "molecular_group", add = "jitter", legend="none")+ rotate_x_text(angle = 45)+ geom_hline(yintercept = mean(myeloma$DEPDC1), linetype=2)+# Add horizontal line at base mean stat_compare_means(method = "anova", label.y = 1600)+ # Add global annova p-value stat_compare_means(label = "p.signif", method = "t.test", ref.group = ".all.")# Pairwise comparison against all
从图中可以看出,DEPDC1基因在Proliferation组中显著性地过表达,而在Hyperdiploid和Low bone disease显著性地低表达
我们也可以将非显著性标记ns去掉,只需要将参数hide.ns=TRUE
ggboxplot(myeloma, x="molecular_group", y="DEPDC1", color = "molecular_group", add = "jitter", legend="none")+ rotate_x_text(angle = 45)+ geom_hline(yintercept = mean(myeloma$DEPDC1), linetype=2)+# Add horizontal line at base mean stat_compare_means(method = "anova", label.y = 1600)+ # Add global annova p-value stat_compare_means(label = "p.signif", method = "t.test", ref.group = ".all.", hide.ns = TRUE)# Pairwise comparison against all
多个分组变量
按另一个变量进行分组之后进行统计检验,比如按变量dose进行分组:
compare_means(len~supp, data=ToothGrowth, group.by = "dose")
#可视化 p <- ggboxplot(ToothGrowth, x="supp", y="len", color = "supp", palette = "jco", add = "jitter", facet.by = "dose", short.panel.labs = FALSE)#按dose进行分面 #label只绘制 p-valuep+stat_compare_means(label = "p.format")
#label绘制显著性水平 p+stat_compare_means(label = "p.signif", label.x = 1.5)
#将所有箱线图绘制在一个panel中 p <- ggboxplot(ToothGrowth, x="dose", y="len", color = "supp", palette = "jco", add = "jitter") p+stat_compare_means(aes(group=supp))
#只显示p-value p+stat_compare_means(aes(group=supp), label = "p.format")
#显示显著性水平 p+stat_compare_means(aes(group=supp), label = "p.signif")
进行paired sample检验 compare_means(len~supp, data=ToothGrowth, group.by = "dose", paired = TRUE)
#可视化 p <- ggpaired(ToothGrowth, x="supp", y="len", color = "supp", palette = "jco", line.color="gray", line.size=0.4, facet.by = "dose", short.panel.labs = FALSE)#按dose分面 #只显示p-value p+stat_compare_means(label = "p.format", paired = TRUE)
其他图形
条形图与线图(一个分组变量)
#有误差棒的条形图,实际上我以前的文章里有纯粹用ggplot2实现 ggbarplot(ToothGrowth, x="dose", y="len", add = "mean_se")+ stat_compare_means()+ stat_compare_means(ref.group = "0.5", label = "p.signif", label.y = c(22, 29))
#有误差棒的线图 ggline(ToothGrowth, x="dose", y="len", add = "mean_se")+ stat_compare_means()+ stat_compare_means(ref.group = "0.5", label = "p.signif", label.y = c(22, 29))
条形图与线图(两个分组变量)
ggbarplot(ToothGrowth, x="dose", y="len", add = "mean_se", color = "supp", palette = "jco", position = position_dodge(0.8))+ stat_compare_means(aes(group=supp), label = "p.signif", label.y = 29)
ggline(ToothGrowth, x="dose", y="len", add = "mean_se", color = "supp", palette = "jco")+ stat_compare_means(aes(group=supp), label = "p.signif", label.y = c(16, 25, 29))
Sessioninfo
sessionInfo() ## R version 3.4.0 (2017-04-21) ## Platform: x86_64-w64-mingw32/x64 (64-bit) ## Running under: Windows 8.1 x64 (build 9600) ## ## Matrix products: default ## ## locale: ## [1] LC_COLLATE=Chinese (Simplified)_China.936 ## [2] LC_CTYPE=Chinese (Simplified)_China.936 ## [3] LC_MONETARY=Chinese (Simplified)_China.936 ## [4] LC_NUMERIC=C ## [5] LC_TIME=Chinese (Simplified)_China.936 ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] survminer_0.4.0 ggpubr_0.1.3 magrittr_1.5 ggplot2_2.2.1 ## ## loaded via a namespace (and not attached): ## [1] Rcpp_0.12.11 compiler_3.4.0 plyr_1.8.4 ## [4] tools_3.4.0 digest_0.6.12 evaluate_0.10 ## [7] tibble_1.3.3 gtable_0.2.0 nlme_3.1-131 ## [10] lattice_0.20-35 rlang_0.1.1 Matrix_1.2-10 ## [13] psych_1.7.5 ggsci_2.4 DBI_0.6-1 ## [16] cmprsk_2.2-7 yaml_2.1.14 parallel_3.4.0 ## [19] gridExtra_2.2.1 dplyr_0.5.0 stringr_1.2.0 ## [22] knitr_1.16 survMisc_0.5.4 rprojroot_1.2 ## [25] grid_3.4.0 data.table_1.10.4 KMsurv_0.1-5 ## [28] R6_2.2.1 km.ci_0.5-2 survival_2.41-3 ## [31] foreign_0.8-68 rmarkdown_1.5 reshape2_1.4.2 ## [34] tidyr_0.6.3 purrr_0.2.2.2 splines_3.4.0 ## [37] backports_1.1.0 scales_0.4.1 htmltools_0.3.6 ## [40] assertthat_0.2.0 mnormt_1.5-5 xtable_1.8-2 ## [43] colorspace_1.3-2 ggsignif_0.2.0 labeling_0.3 ## [46] stringi_1.1.5 lazyeval_0.2.0 munsell_0.4.3 ## [49] broom_0.4.2 zoo_1.8-0
来源:https://www.cnblogs.com/xiaojikuaipao/p/7862990.html