ggpubr包系列学习教程(七 )
2018-09-09 本文已影响18人
Davey1220
使用ggmaplot函数绘制MA图
加载所需R包
library(ggpubr)
基本用法：
Usage
ggmaplot(data, fdr = 0.05, fc = 1.5, genenames = NULL,
detection_call = NULL, size = NULL, font.label = c(12, "plain", "black"),
label.rectangle = FALSE, palette = c("#B31B21", "#1465AC", "darkgray"),
top = 15, select.top.method = c("padj", "fc"), main = NULL,
xlab = "Log2 mean expression", ylab = "Log2 fold change",
ggtheme = theme_classic(), ...)
常用参数：
Arguments
data #差异基因分析结果 an object of class DESeqResults, get_diff, DE_Results, matrix or data frame containing the columns baseMean, log2FoldChange, and padj. Rows are genes.
#baseMean: the mean expression of genes in the two groups.
#log2FoldChange: the log2 fold changes of group 2 compared to group 1
#padj: the adjusted p-value of the used statiscal test.
fdr #设定fdr阈值 Accepted false discovery rate for considering genes as differentially expressed.
fc #设定fc阈值 the fold change threshold. Only genes with a fold change >= fc and padj <= fdr are considered as significantly differentially expressed.
genenames #基因名 a character vector of length nrow(data) specifying gene names corresponding to each row. Used for point labels.
detection_call #选出特定表达模式的基因进行展示 a numeric vector with length = nrow(data), specifying if the genes is expressed (value = 1) or not (value = 0). For example detection_call = c(1, 1, 0, 1, 0, 1). Default is NULL. If detection_call column is available in data, it will be used.
size #points size.
font.label #a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of point labels. For example font.label = c(14, "bold", "red").
label.rectangle #logical value. If TRUE, add rectangle underneath the text, making it easier to read.
palette #the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
top #选定top基因进行展示 the number of top genes to be shown on the plot. Use top = 0 to hide to gene labels.
select.top.method #methods to be used for selecting top genes. Allowed values include "padj" and "fc" for selecting by adjusted p values or fold changes, respectively.
main #plot main title.
xlab #character vector specifying x axis labels. Use xlab = FALSE to hide xlab.
ylab #character vector specifying y axis labels. Use ylab = FALSE to hide ylab.
ggtheme #function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void()
... #other arguments to be passed to ggpar.
使用示例
Examples
# 加载数据集
data(diff_express)
head(diff_express)
## name baseMean log2FoldChange padj
## ENSG00000000003 TSPAN6 0.1184475 0.0000000 NA
## ENSG00000000419 DPM1 1654.4618144 0.6789538 5.280802e-02
## ENSG00000000457 SCYL3 681.0463277 1.5263838 3.915112e-07
## ENSG00000000460 C1orf112 389.7226640 3.8933573 1.180333e-14
## ENSG00000000938 FGR 364.7810090 -2.3554014 1.559228e-04
## ENSG00000000971 CFH 1.1346239 1.2932740 4.491812e-01
## detection_call
## ENSG00000000003 0
## ENSG00000000419 1
## ENSG00000000457 1
## ENSG00000000460 1
## ENSG00000000938 1
## ENSG00000000971 0
# Default plot
p1 <- ggmaplot(diff_express, fdr = 0.05, fc = 2, size = 0.4,
palette = c("red","green","gray"))
p1
p1
p2 <- ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"),
fdr = 0.05, fc = 2, size = 0.4,
palette = c("#B31B21", "#1465AC", "darkgray"),
genenames = as.vector(diff_express$name),
xlab = "M",ylab = "A",
legend = "top", top = 20,
font.label = c("bold", 11),
font.legend = "bold",
font.main = "bold",
ggtheme = ggplot2::theme_minimal())
p2
p2
# Add rectangle around labels
p3 <- ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"),
fdr = 0.05, fc = 2, size = 0.4,
palette = c("#B31B21", "#1465AC", "darkgray"),
genenames = as.vector(diff_express$name),
legend = "top", top = 20,
font.label = c("bold", 11), label.rectangle = TRUE,
font.legend = "bold", select.top.method = "padj",
font.main = "bold",
ggtheme = ggplot2::theme_minimal())
p3
p3
p4 <- ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"),
fdr = 0.05, fc = 2, size = 0.5,
palette = c("#B31B21", "#1465AC", "darkgray"),
genenames = as.vector(diff_express$name),
legend = "top", top = 20, select.top.method = "fc",
font.label = c("bold", 11), label.rectangle = TRUE,
font.legend = "bold",
font.main = "bold",
ggtheme = ggplot2::theme_minimal())
p4
p4
参考来源：
https://www.rdocumentation.org/packages/ggpubr/versions/0.1.4/topics/ggmaplot
sessionInfo()
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: OS X El Capitan 10.11.3
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggpubr_0.1.7.999 magrittr_1.5 ggplot2_3.0.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.18 rstudioapi_0.7 bindr_0.1.1 knitr_1.20
## [5] tidyselect_0.2.4 munsell_0.5.0 colorspace_1.3-2 R6_2.2.2
## [9] rlang_0.2.2 stringr_1.3.1 plyr_1.8.4 dplyr_0.7.6
## [13] tools_3.5.1 grid_3.5.1 gtable_0.2.0 withr_2.1.2
## [17] htmltools_0.3.6 assertthat_0.2.0 yaml_2.2.0 lazyeval_0.2.1
## [21] rprojroot_1.3-2 digest_0.6.16 tibble_1.4.2 crayon_1.3.4
## [25] bindrcpp_0.2.2 purrr_0.2.5 ggrepel_0.8.0 glue_1.3.0
## [29] evaluate_0.11 rmarkdown_1.10 labeling_0.3 stringi_1.2.4
## [33] compiler_3.5.1 pillar_1.3.0 scales_1.0.0 backports_1.1.2
## [37] pkgconfig_2.0.2
