R画网络图

R  画网络图

目的：用R做生信分析，画基因样本的网络图，从中观察样本的致病性情况。

 

一、所用到的包

1. library(tidyr)
2. library(ggplot2)
3. library(reshape2)
4. library(readr)
5. library(network)
6. library(dplyr)
7. library(plyr)
8. library(sna)
9. library(GGally)
10. library(ggnetwork)
11. library(tidygraph)# tidy graph analysis
12. #library(tidyverse)# tidy data analysis
13. library(ggraph)
14. library(stringr)
15. library(networkD3)
16. library(igraph)
17. library(visNetwork)
18. library(threejs)
19. library(ndtv)
20. library(grid)  
21. library(Rmisc)
22. #library(vioplot)
23. library(tibble)

 

13行中：tidyverse包集成了很多画图的包：如下

tidyverse_packages(include_self = TRUE)

 [1] "broom"       "cli"         "crayon"      "dplyr"       "dbplyr"      "forcats"     "ggplot2"     "haven"       "hms"         "httr"       

[11] "jsonlite"    "lubridate"   "magrittr"    "modelr"      "purrr"       "readr"       "readxl\n(>=" "reprex"      "rlang"       "rstudioapi"

[21] "rvest"       "stringr"     "tibble"      "tidyr"       "xml2"        "tidyverse"  

 

 

但是如果同时使用这些包，会提示tidyverse_conflicts()，使用tidyverse_conflicts()可以查看tidyverse和其他哪些包冲突：

> tidyverse_conflicts()

-- Conflicts ------------------------------------------ tidyverse_conflicts() --

x tidygraph::arrange()    masks dplyr::arrange(), plyr::arrange()

x tibble::as_data_frame() masks igraph::as_data_frame(), dplyr::as_data_frame()

x purrr::compact()        masks plyr::compact()

x purrr::compose()        masks igraph::compose()

x dplyr::count()          masks plyr::count()

x tidyr::crossing()       masks igraph::crossing()

x dplyr::failwith()       masks plyr::failwith()

x tidygraph::filter()     masks dplyr::filter(), stats::filter()

x igraph::groups()        masks tidygraph::groups(), dplyr::groups()

x dplyr::id()             masks plyr::id()

x dplyr::lag()            masks stats::lag()

x tidygraph::mutate()     masks dplyr::mutate(), plyr::mutate()

x tidygraph::rename()     masks dplyr::rename(), plyr::rename()

x purrr::simplify()       masks igraph::simplify()

x dplyr::summarise()      masks plyr::summarise()

x dplyr::summarize()      masks plyr::summarize()

 

所以我注释掉了tidyverse&