R语言实战——Nature Neuroscience的十年（一）

一只羊

发布于 2019-07-27 18:55:03

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发布于 2019-07-27 18:55:03

文章被收录于专栏：生信了生信了生信了

序

前言

学习R语言有半年时间了，一直想找个机会找个小项目练练手，所以才有了这篇文章。

目的

对《Nature Neuroscience》杂志2009-2018年的研究文章进行可视化初探。

主要分为以下几个部分：

1. 基础统计及可视化

2. 进一步统计及可视化

3. 主要国家比较及可视化

4. 热词统计及可视化

5. 对接收时间的统计建模及特征选择

（截至发文才完成第1和第2部分，其余部分只能有机会再做）

数据来源

从Nature杂志官网搜索文章，搜索参数为：

journal: neuro

subject: biological-sciences/health-sciences

article_type: research, review, protocol（不包括Introduction, Editorial）

time_range: 2009-2018

说明

1. 中国（港澳台地区）与中国大陆合并计算。

2. 如果不做特别说明，日期默认按照发表日期（Publlish Date）统计。

不足

1. 数据缺失或不规范为数据分析带来偏差。比如国家、省份、城市名称前后不一致或缺失。

2. 对NA的处理还不够完善。什么时候该去除NA是要仔细考量的。

3. 有些作者的英文名是重合的，计算时没有做区分。

4. 文章数相同的作者排名是按照姓名的字典序排序的。

5. 没有统计标准差。

6. R作图的一些细节还需要改善。

7. 实现的代码虽然经过简化，但还是有些冗余。

8. 还有很多有意思的东西限于时间经历和篇幅就暂不研究了。

声明

本文仅是个人练习的结果，肯定有谬误的地方，不具有任何参考价值，那些花里胡哨的话不要乱了心！

第一部分：基础统计及可视化

导入数据

数据预处理

观察数据

'data.frame':   2575 obs. of  21 variables:
$ date       : chr  "2018-12-31" "2018-12-17" "2018-12-17" "2018-12-17" ...
$ title      : chr  "Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections" "TDP-43 extracted from frontotemporal lobar degeneration subject brains displays distinct aggregate assemblies a"| __truncated__ "Efficient coding of subjective value" "Invasion of white matter tracts by glioma stem cells is regulated by a NOTCH1–SOX2 positive-feedback loop" ...
$ type       : chr  "Research" "Research" "Research" "Research" ...
$ magzine    : chr  "Nature Neuroscience" "Nature Neuroscience" "Nature Neuroscience" "Nature Neuroscience" ...
$ volume     : int  NA 22 22 22 22 22 22 22 22 22 ...
$ startPage  : int  1 65 134 91 120 57 78 37 106 25 ...
$ endPage    : int  11 77 142 105 133 64 90 46 119 36 ...
$ abstract   : chr  "Analysis of entire transparent rodent bodies after clearing could provide holistic biological information in he"| __truncated__ "Accumulation of abnormally phosphorylated TDP-43 (pTDP-43) is the main pathology in affected neurons of people "| __truncated__ "Preference-based decisions are essential for survival, for instance, when deciding what we should (not) eat. De"| __truncated__ "Early invasive growth along specific anatomical structures, especially the white matter tract, is regarded as o"| __truncated__ ...
$ receiveDate: chr  "2018-04-01" "2018-09-10" "2018-01-20" "2018-04-06" ...
$ reviseDate : chr  "" "" "" "" ...
$ acceptDate : chr  "2018-11-21" "2018-11-14" "2018-11-13" "2018-10-31" ...
$ author     : chr  "Ruiyao Cai|Chenchen Pan|Alireza Ghasemigharagoz|Mihail Ivilinov Todorov|Benjamin F<U+00F6>rstera|Shan Zhao|Hars"| __truncated__ "Florent Laferrière|Zuzanna Maniecka|Manuela Pérez-Berlanga|Marian Hruska-Plochan|Larissa Gilhespy|Eva-Maria Hoc"| __truncated__ "Rafael Polanía|Michael Woodford|Christian C. Ruff" "Jun Wang|Sen-Lin Xu|Jiang-Jie Duan|Liang Yi|Yu-Feng Guo|Yu Shi|Lin Li|Ze-Yu Yang|Xue-Mei Liao|Jiao Cai|Yan-Qi Z"| __truncated__ ...
$ nauthor    : int  22 23 3 22 4 10 18 17 20 15 ...
$ ncoauthor  : int  2 2 1 4 1 1 3 1 2 1 ...
$ corresp    : chr  "Ali Ertürk" "Magdalini Polymenidou" "Rafael Polanía|Christian C. Ruff" "Xiu-Wu Bian|Shi-Cang Yu" ...
$ ncorresp   : int  1 1 2 2 1 2 2 1 3 2 ...
$ institute  : chr  "Ludwig-Maximilians University Munich;Graduate School of Systemic Neurosciences Munich|Ludwig-Maximilians Univer"| __truncated__ "University of Zurich|University of Zurich|University of Zurich|University of Zurich|University of Zurich|Univer"| __truncated__ "University of Zurich;ETH Zurich;Columbia University|Columbia University|University of Zurich" "Army Medical University (Third Military Medical University);Army Medical University (Third Military Medical Uni"| __truncated__ ...
$ city       : chr  "Munich;Munich|Munich;Munich|Munich|Munich;Munich|Munich|Munich|Munich|Munich|Munich|Munich;Munich|Munich|Copenh"| __truncated__ "Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|London;London|London;London|London;London"| __truncated__ "Zurich;Zurich;New York|New York|Zurich" "Chongqing;Chongqing|Chongqing|Chongqing;Chongqing|Chongqing|Chongqing;Chongqing|Chongqing|Chongqing;Chongqing|C"| __truncated__ ...
$ province   : chr  "Munich;Munich|Munich;Munich|Munich|Munich;Munich|Munich|Munich|Munich|Munich|Munich|Munich;Munich|Munich|Copenh"| __truncated__ "Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|Zurich|London;London|London;London|London;London"| __truncated__ "Zurich;Zurich;NY|NY|Zurich" "Chongqing;Chongqing|Chongqing|Chongqing;Chongqing|Chongqing|Chongqing;Chongqing|Chongqing|Chongqing;Chongqing|C"| __truncated__ ...
$ country    : chr  "Germany;Germany|Germany;Germany|Germany|Germany;Germany|Germany|Germany|Germany|Germany|Germany|Germany;Germany"| __truncated__ "Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Switzerland|Swi"| __truncated__ "Switzerland;Switzerland;USA|USA|Switzerland" "China;China|China|China;China|China|China;China|China|China;China|China;China|China;China|China;China|China|Chi"| __truncated__ ...
$ address    : chr  "Institute for Stroke and Dementia Research, Klinikum der Universit<U+00E4>t München, Ludwig-Maximilians Univers"| __truncated__ "Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland|Institute of Molecular Life Sci"| __truncated__ "Zurich Center for Neuroeconomics (ZNE), Department of Economics, University of Zurich, Zurich, Switzerland;Deci"| __truncated__ "Institute of Pathology and Southwest Cancer Center, Key Laboratory of the Ministry of Education, Southwest Hosp"| __truncated__ ...

转换数据类型

看各列是否有NA

       date       title        type     magzine      volume   startPage
         0           0           0           0           1           0
   endPage    abstract receiveDate  reviseDate  acceptDate      author
         0           0          87        2574          87           0
   nauthor   ncoauthor     corresp    ncorresp   institute        city
         0           0           9           0           0           0
  province     country     address
         0           0           0