{"id":483,"date":"2020-11-03T12:17:37","date_gmt":"2020-11-03T11:17:37","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=483"},"modified":"2022-04-06T14:50:45","modified_gmt":"2022-04-06T12:50:45","slug":"r-survival-manual","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/r-survival-manual\/","title":{"rendered":"Tutorials &#8211; R survival manual"},"content":{"rendered":"<h2>R tutorial<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">A step by step guide to start on R<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">christine Tranchant-Dubreuil (christine.tranchant@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">21\/09\/2018<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">22\/09\/2018<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Summary<\/h3>\n<p><!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 --><\/p>\n<ul>\n<li>\n<p><a href=\"#start\">Starting slowly on R<\/a><\/p>\n<ul>\n<li><a href=\"#install\">Installing new packages <code>install.packages(packages)<\/code><\/a><\/li>\n<li><a href=\"#library\">Loading library<code>library<\/code><\/a><\/li>\n<li><a href=\"#setwd\">Setting a working directory<\/a><\/li>\n<li><a href=\"#getwd\">Getting the current working directory <code>getwd<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#importCsv\">Importing Data From <code>csv<\/code> File Into a <code>Dataframe<\/code><\/a><\/p>\n<ul>\n<li><a href=\"#readCsv\">Storing the content of a file <em>allGenomeVersion.csv<\/em> into a dataframe <em>myGenome<\/em> - <code>read.csv2()<\/code> (french format)<\/a><\/li>\n<li><a href=\"#printDF\">Displaying the whole dataframe<\/a><\/li>\n<li><a href=\"#getType\">Getting the type - <code>class(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#structureDF\">Getting the structure of the dataframe (data type, number of levels) - <code>str(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#statDF\">Getting basic stats about te content of a dataframe - <code>summary(dataframe)<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#info\">Displaying basic informations about the dataframe structure<\/a><\/p>\n<ul>\n<li><a href=\"#colnames\">Column names - <code>names(dataframe)<\/code> or  <code>colnames(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#dim\">Lines and columns number - <code>dim(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#nrow\">Lines number - <code>nrow(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#ncol\">Columns number - <code>ncol(dataframe)<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#print\">Displaying the dataframe content<\/a><\/p>\n<ul>\n<li><a href=\"#head\">Printing the first lines - <code>head(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#last\">Printing the last lines - <code>last(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#df0\">Printing a column - <code>dataframe[colNum|colName]<\/code> or  <code>dataframe$colName<\/code><\/a><\/li>\n<li><a href=\"#df\">Printing one whole line - <code>dataframe[lineNum,]<\/code><\/a><\/li>\n<li><a href=\"#df2\">Printing one line, one column - <code>dataframe[lineNum,colNum]<\/code><\/a><\/li>\n<li><a href=\"#df3\">Printing some lines - <code>dataframe[LineStart:LineEnd,]<\/code><\/a><\/li>\n<li><a href=\"#df4\">Printing one column of some lines - <code>dataframe[c(line1,line2,line3),colNum]<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#manipulating\">Manipulating the content of a dataframe<\/a><\/p>\n<ul>\n<li><a href=\"#add\">Adding a new column<\/a><\/li>\n<li><a href=\"#unique\">Extracting unique values of a column - <code>unique(dataframe$colName)<\/code><\/a><\/li>\n<li><a href=\"#extract\">Extracting one part of a dataframe - <code>subset(dataframe)<\/code><\/a><\/li>\n<li><a href=\"#cal\">Calculating a sum - <code>sum(dataframe)<\/code> with filtering on an other column<\/a><\/li>\n<li><a href=\"#length\"> Getting the number of elements in a dataframe - <code>length(dataframe)<\/code> with filtering on an other column<\/a><\/li>\n<li><a href=\"#order\">Ordering dataframe on one column<\/a><\/li>\n<li><a href=\"#summary\">Getting summaries of values of a column  - <code>summary<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#plot\">Plotting data from a dataframe with <code>ggplot<\/code> library<\/a><\/p>\n<ul>\n<li><a href=\"#barplot\">Creating a barplot with <code>geom_bar(stat = &quot;identity&quot;)<\/code><\/a><\/li>\n<li><a href=\"#flip\">Distinct plot - <code>position=position_dodge()<\/code> and flip plot with <code>coord_flip()<\/code><\/a><a name=\"dodge\"><\/a><\/li>\n<li><a href=\"#savePng\">Save into a file`<\/a><\/li>\n<li><a href=\"#count\">Creating a barplot with <code>geom_bar(stat = &quot;count&quot;)<\/code><\/a><\/li>\n<li><a href=\"#violinPlot\"> Plotting a violin plot  - <code>geom_violin()<\/code><\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<p><a href=\"#license\">License<\/a> <\/p>\n<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"start\"><\/a><\/p>\n<h3>Starting slowly on R<\/h3>\n<p><a name=\"install\"><\/a><\/p>\n<h5>Installing New Packages\/libraries - <code>install.packages(package) <\/code><\/h5>\n<pre><code>>install.packages(&#039;ggplot2&#039;)<\/code><\/pre>\n<p><a name=\"library\"><\/a><\/p>\n<h5>Loading libraries  - <code>library(package)<\/code><\/h5>\n<pre><code>>library(ggplot2) # plot\n>library(scales)  # plot scales\n>library(stringr) # str_detect\n>library(gridExtra) # grid`<\/code><\/pre>\n<p><a name=\"setwd\"><\/a><\/p>\n<h5>Setting a Working Directory <code>setwd(path)<\/code><\/h5>\n<pre><code>>setwd(\/users\/tranchan\/riceAnalysis)<\/code><\/pre>\n<p><a name=\"getwd\"><\/a><\/p>\n<h5>Getting the current Working Directory <code>getwd()<\/code><\/h5>\n<pre><code>>getwd()\n[1] &quot;\/Users\/tranchan\/Documents\/Bioanalyse\/panGenome&quot;<\/code><\/pre>\n<hr \/>\n<p><a name=\"importCsv\"><\/a><\/p>\n<h3>Importing Data From <code>csv<\/code> File Into a <code>Dataframe<\/code><\/h3>\n<p><a name=\"readCsv\"><\/a><\/p>\n<h5>Storing a file <em>allGenomeVersion.csv<\/em> into the dataframe <em>myGenome<\/em> - <code>read.csv2()<\/code> (french format)<\/h5>\n<pre><code>#File with 6 columns and 2010 lines\nName    Type    Length  %GC Organism    Type\nChr01   N   32613412    43.53   dna:chromosome  v1\nChr01   N   39656875    43.05   dna:chromosome  v2\nChr02   N   29142869    43.19   dna:chromosome  v1\nChr02   N   34451706    42.81   dna:chromosome  v2\nChr03   N   33053699    43.20   dna:chromosome  v1\nChr03   N   35526804    43.23   dna:chromosome  v2\nChr04   N   26299011    43.54   dna:chromosome  v1\nChr04   N   31572834    43.19   dna:chromosome  v2\nChr05   N   23192814    42.91   dna:chromosome  v1\nChr05   N   26274045    42.82   dna:chromosome  v2\nChr06   N   24174485    42.90   dna:chromosome  v1\nChr06   N   29275208    42.90   dna:chromosome  v2\nChr07   N   21799424    43.09   dna:chromosome  v1\nChr07   N   26599614    42.82   dna:chromosome  v2\nChr08   N   20292731    42.97   dna:chromosome  v1\nChr08   N   25472747    42.64   dna:chromosome  v2\nChr09   N   17607432    43.51   dna:chromosome  v1\nChr09   N   21796211    42.91   dna:chromosome  v2\nChr10   N   16910673    43.10   dna:chromosome  v1\nChr10   N   22418184    42.96   dna:chromosome  v2\nChr11   N   20796451    42.59   dna:chromosome  v1\nChr11   N   26393634    42.28   dna:chromosome  v2\nChr12   N   19154523    42.47   dna:chromosome  v1\nChr12   N   25020143    42.38   dna:chromosome  v2\nADWL01002872.1  N   9871    37.93   dna:scaffold    v1\nADWL01002880.1  N   2202    52.91   dna:scaffold    v1\nADWL01002881.1  N   2284    63.09   dna:scaffold    v1\n....\n<\/code><\/pre>\n<pre><code>>myGenome &lt;- read.csv2(&quot;allGenomeVersion.csv&quot;,header = TRUE)<\/code><\/pre>\n<p><a name=\"printDF\"><\/a><\/p>\n<h5>Displaying the whole dataframe<\/h5>\n<pre><code>>myGenome\n\nName  Type  Length  X.GC  Organism  Type.1\nChr10   N   16910673    43.10   dna:chromosome  v1\nChr09   N   17607432    43.51   dna:chromosome  v1\nChr12   N   19154523    42.47   dna:chromosome  v1\nChr08   N   20292731    42.97   dna:chromosome  v1\nChr11   N   20796451    42.59   dna:chromosome  v1\nChr07   N   21799424    43.09   dna:chromosome  v1\n....<\/code><\/pre>\n<p><a name=\"getType\"><\/a><\/p>\n<h5>Get the type - <code>class(dataframe)<\/code><\/h5>\n<pre><code>>class(myGenome)\n[1] &quot;data.frame&quot;<\/code><\/pre>\n<p><a name=\"structureDF\"><\/a><\/p>\n<h5>Get the structure of the dataframe (data type, number of levels) - <code>str(dataframe)<\/code><\/h5>\n<pre><code>>str(myGenome) \n&#039;data.frame&#039;: 2010 obs. of  6 variables:\n $ Name    : Factor w\/ 1998 levels &quot;ADWL01002872.1&quot;,..: 1210 1209 1212 1208 1211 1207 1205 1206 1204 1202 ...\n $ Type    : Factor w\/ 1 level &quot;N&quot;: 1 1 1 1 1 1 1 1 1 1 ...\n $ Length  : int  16910673 17607432 19154523 20292731 20796451 21799424 23192814 24174485 26299011 29142869 ...\n $ X.GC    : Factor w\/ 1191 levels &quot;26.08&quot;,&quot;30.70&quot;,..: 512 547 454 499 466 511 493 492 550 520 ...\n $ Organism: Factor w\/ 2 levels &quot;dna:chromosome&quot;,..: 1 1 1 1 1 1 1 1 1 1 ...\n $ Type.1  : Factor w\/ 2 levels &quot;v1&quot;,&quot;v2&quot;: 1 1 1 1 1 1 1 1 1 1 ...<\/code><\/pre>\n<p><a name=\"statDF\"><\/a><\/p>\n<h5>Get basics stats about dataframe content - <code>summary(dataframe)<\/code><\/h5>\n<pre><code>>summary(myGenome)\n      Name      Type         Length              X.GC                Organism    Type.1   \n Chr01  :   2   N:2010   Min.   :    1026   44.90  :   7   dna:chromosome:  24   v1:1951  \n Chr02  :   2            1st Qu.:    3229   41.27  :   6   dna:scaffold  :1986   v2:  59  \n Chr03  :   2            Median :    5742   41.73  :   6                                  \n Chr04  :   2            Mean   :  330219   42.82  :   6                                  \n Chr05  :   2            3rd Qu.:   13154   42.91  :   6                                  \n Chr06  :   2            Max.   :39656875   43.00  :   6                                  \n (Other):1998                               (Other):1973  <\/code><\/pre>\n<hr \/>\n<p><a name=\"info\"><\/a><\/p>\n<h3>Displaying basic informations about the dataframe structure<\/h3>\n<p><a name=\"colnames\"><\/a><\/p>\n<h5>Column names - <code>names(dataframe)<\/code> or  <code>colnames(dataframe)<\/code><\/h5>\n<pre><code>> names(myGenome)\n[1] &quot;Name&quot;     &quot;Type&quot;     &quot;Length&quot;   &quot;X.GC&quot;     &quot;Organism&quot; &quot;Type.1&quot;  \n\n> colnames(myGenome)\n[1] &quot;Name&quot;     &quot;Type&quot;     &quot;Length&quot;   &quot;X.GC&quot;     &quot;Organism&quot; &quot;Type.1&quot;  <\/code><\/pre>\n<p><a name=\"dim\"><\/a><\/p>\n<h5>Lines and columns number - <code>dim(dataframe)<\/code><\/h5>\n<pre><code>> dim(myGenome) \n[1] 2010    6<\/code><\/pre>\n<p><a name=\"nrow\"><\/a><\/p>\n<h5>Lines number - <code>nrow(dataframe)<\/code><\/h5>\n<pre><code>> nrow(myGenome)\n[1] 2010<\/code><\/pre>\n<p><a name=\"ncol\"><\/a><\/p>\n<h5>Columns number - <code>ncol(dataframe)<\/code>]<\/h5>\n<pre><code>> ncol(myGenome)\n[1] 6<\/code><\/pre>\n<hr \/>\n<p><a name=\"print\"><\/a><\/p>\n<h3>Displaying and manipulating the dataframe content<\/h3>\n<p><a name=\"head\"><\/a><\/p>\n<h5>Printing the first lines - <code>head(dataframe)<\/code><\/h5>\n<pre><code>> head(myGenome)\n   Name Type   Length  X.GC       Organism Type.1\n1 Chr10    N 16910673 43.10 dna:chromosome     v1\n2 Chr09    N 17607432 43.51 dna:chromosome     v1\n3 Chr12    N 19154523 42.47 dna:chromosome     v1\n4 Chr08    N 20292731 42.97 dna:chromosome     v1\n5 Chr11    N 20796451 42.59 dna:chromosome     v1\n6 Chr07    N 21799424 43.09 dna:chromosome     v1\n\n> head(myGenome,n=2)\n   Name Type   Length  X.GC       Organism Type.1\n1 Chr10    N 16910673 43.10 dna:chromosome     v1\n2 Chr09    N 17607432 43.51 dna:chromosome     v1<\/code><\/pre>\n<p><a name=\"last\"><\/a><\/p>\n<h5>Printing the last lines - <code>last(dataframe)<\/code><\/h5>\n<pre><code>> tail(myGenome)\n            Name Type Length  X.GC     Organism Type.1\n2005 ChrUN-Ctg78    N  21053 43.05 dna:scaffold     v2\n2006 ChrUN-Ctg79    N  19363 40.63 dna:scaffold     v2\n2007 ChrUN-Ctg80    N  15054 41.18 dna:scaffold     v2\n2008 ChrUN-Ctg81    N  13998 42.98 dna:scaffold     v2\n2009 ChrUN-Ctg82    N  13471 42.29 dna:scaffold     v2\n2010 ChrUN-Ctg83    N  10534 42.37 dna:scaffold     v2\n\n> tail(myGenome,n=1)\n            Name Type Length  X.GC     Organism Type.1\n2010 ChrUN-Ctg83    N  10534 42.37 dna:scaffold     v2<\/code><\/pre>\n<p><a name=\"df0\"><\/a><\/p>\n<h5>Printing a column - <code>dataframe[colNum|colName]<\/code> or  <code>dataframe$colName<\/code><\/h5>\n<ul>\n<li>output result (line)<\/li>\n<\/ul>\n<pre><code>> head(myGenome[,&quot;Length&quot;])\n[1] 16910673 17607432 19154523 20292731 20796451 21799424\n<\/code><\/pre>\n<pre><code>> head(myGenome$Length) \n[1] 16910673 17607432 19154523 20292731 20796451 21799424\n<\/code><\/pre>\n<ul>\n<li>output result (column)<\/li>\n<\/ul>\n<pre><code>> head(myGenome[1])\n   Name\n1 Chr10\n2 Chr09\n3 Chr12\n4 Chr08\n5 Chr11\n6 Chr07<\/code><\/pre>\n<pre><code>> head(myGenome[&#039;Length&#039;])\n    Length\n1 16910673\n2 17607432\n3 19154523\n4 20292731\n5 20796451\n6 21799424<\/code><\/pre>\n<p><a name=\"df\"><\/a><\/p>\n<h5>Printing one whole line - <code>dataframe[lineNum,] <\/code><\/h5>\n<p>Line 2<\/p>\n<pre><code>> myGenome[2,]\n   Name Type   Length  X.GC       Organism Type.1\n2 Chr09    N 17607432 43.51 dna:chromosome     v1<\/code><\/pre>\n<p><a name=\"df2\"><\/a><\/p>\n<h5>Printing one line, one column - <code>dataframe[lineNum,colNum]<\/code><\/h5>\n<p>Line 2, column 6 then line 2, column 3<\/p>\n<pre><code>> myGenome[2,6]\n[1] v1\nLevels: v1 v2\n\n> myGenome[2,3]\n[1] 17607432<\/code><\/pre>\n<p><a name=\"df3\"><\/a><\/p>\n<h5>Printing some lines - <code>dataframe[LineStart:LineEnd,]<\/code><\/h5>\n<pre><code>> myGenome[1:3,]\n   Name Type   Length  X.GC       Organism Type.1\n1 Chr10    N 16910673 43.10 dna:chromosome     v1\n2 Chr09    N 17607432 43.51 dna:chromosome     v1\n3 Chr12    N 19154523 42.47 dna:chromosome     v1\n\n> myGenome[10:15,]\n    Name Type   Length  X.GC       Organism Type.1\n10 Chr02    N 29142869 43.19 dna:chromosome     v1\n11 Chr01    N 32613412 43.53 dna:chromosome     v1\n12 Chr03    N 33053699 43.20 dna:chromosome     v1\n13 Chr01    N 39656875 43.05 dna:chromosome     v2\n14 Chr02    N 34451706 42.81 dna:chromosome     v2\n15 Chr03    N 35526804 43.23 dna:chromosome     v2<\/code><\/pre>\n<p><a name=\"df4\"><\/a><\/p>\n<h5>Printing one column of some lines - <code>dataframe[c(line1,line2,line3),colNum]<\/code><\/h5>\n<p>Print the complete lines 1, 3, 7, 6 then just the column 3 of the same lines<\/p>\n<pre><code>> myGenome[c(1,3,7,6),]\n   Name Type   Length  X.GC       Organism Type.1\n1 Chr10    N 16910673 43.10 dna:chromosome     v1\n3 Chr12    N 19154523 42.47 dna:chromosome     v1\n7 Chr05    N 23192814 42.91 dna:chromosome     v1\n6 Chr07    N 21799424 43.09 dna:chromosome     v1\n\n> myGenome[c(1,3,7,6),3]\n[1] 16910673 19154523 23192814 21799424\n<\/code><\/pre>\n<hr \/>\n<p><a name=\"manipulating\"><\/a><\/p>\n<h3>Manipulating the content of a dataframe<\/h3>\n<p><a name=\"add\"><\/a><\/p>\n<h5>Adding a new column<\/h5>\n<ul>\n<li>A new collumn firstly filled with &quot;NA&quot;\n<pre><code>\n> myGenome[&quot;mb&quot;] &lt;- NA <\/code><\/pre>\n<\/li>\n<\/ul>\n<blockquote>\n<p>head(myGenome)<br \/>\nName Type   Length  X.GC       Organism Type.1 mb<br \/>\n1 Chr10    N 16910673 43.10 dna:chromosome     v1 NA<br \/>\n2 Chr09    N 17607432 43.51 dna:chromosome     v1 NA<br \/>\n3 Chr12    N 19154523 42.47 dna:chromosome     v1 NA<br \/>\n4 Chr08    N 20292731 42.97 dna:chromosome     v1 NA<br \/>\n5 Chr11    N 20796451 42.59 dna:chromosome     v1 NA<br \/>\n6 Chr07    N 21799424 43.09 dna:chromosome     v1 NA<\/p>\n<pre><code><\/code><\/pre>\n<\/blockquote>\n<ul>\n<li>The new column receives the result of an operation\n<pre><code>\n> myGenome$mb &lt;- as.integer(myGenome$Length\/1000000)<\/code><\/pre>\n<\/li>\n<\/ul>\n<blockquote>\n<p>head(myGenome)<br \/>\nName Type   Length  X.GC       Organism Type.1 mb<br \/>\n1 Chr10    N 16910673 43.10 dna:chromosome     v1 16<br \/>\n2 Chr09    N 17607432 43.51 dna:chromosome     v1 17<br \/>\n3 Chr12    N 19154523 42.47 dna:chromosome     v1 19<br \/>\n4 Chr08    N 20292731 42.97 dna:chromosome     v1 20<br \/>\n5 Chr11    N 20796451 42.59 dna:chromosome     v1 20<br \/>\n6 Chr07    N 21799424 43.09 dna:chromosome     v1 21<\/p>\n<pre><code><\/code><\/pre>\n<\/blockquote>\n<p><a name=\"unique\"><\/a><\/p>\n<h5>Extracting unique values of a column - <code>unique(dataframe$colName)<\/code><\/h5>\n<pre><code>> myGenome$Organism\n   [1] dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome\n   [8] dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome\n  [15] dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome dna:chromosome\n  [22] dna:chromosome dna:chromosome dna:chromosome dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n  [29] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n  [36] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n  [43] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n  [50] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n  [57] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n  [64] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n ... \n [981] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n [988] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n [995] dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold   dna:scaffold  \n [ reached getOption(&quot;max.print&quot;) -- omitted 1010 entries ]\nLevels: dna:chromosome dna:scaffold\n\n> unique(myRef$Organism)\n[1] dna:chromosome dna:scaffold  \nLevels: dna:chromosome dna:scaffold\n\n> unique(myGenomef$Type.1)\n[1] v1 v2\nLevels: v1 v2<\/code><\/pre>\n<p><a name=\"extract\"><\/a><\/p>\n<h5>Extracting one part of a dataframe into a new dataframe - <code>subset(dataframe)<\/code><\/h5>\n<ul>\n<li>Extract only lines about chromosome (Organism column equals to &quot;dna:chromosome&quot;) - <code>==<\/code><\/li>\n<\/ul>\n<pre><code>> myGenomeSubset &lt;- subset(myGenome, Organism==&quot;dna:chromosome&quot;)\n> head(myrefGenome)\n\n> myrefSubset &lt;- subset(myGenome, Organism==&quot;dna:chromosome&quot;)\n> head(myrefGenome)\n   Name Type   Length  X.GC       Organism Type.1 mb\n1 Chr10    N 16910673 43.10 dna:chromosome     v1 16\n2 Chr09    N 17607432 43.51 dna:chromosome     v1 17\n3 Chr12    N 19154523 42.47 dna:chromosome     v1 19\n4 Chr08    N 20292731 42.97 dna:chromosome     v1 20\n5 Chr11    N 20796451 42.59 dna:chromosome     v1 20\n6 Chr07    N 21799424 43.09 dna:chromosome     v1 21\n\n> dim(myRGenome)\n[1] 2010    7\n\n> dim(myGenomeSubset)\n[1] 24  7\n<\/code><\/pre>\n<ul>\n<li>Extract only lines about scaffold (Organism column not equals to &quot;dna:chromosome&quot;) - <code>!=<\/code><\/li>\n<\/ul>\n<pre><code>> myScaffSubset &lt;- subset(myRef, Organism!=&quot;dna:chromosome&quot;)\n\n> head(myScaffSubset)\n                  Name Type Length  X.GC     Organism Type.1 mb\n25 Oglab05_unplaced019    N   1026 54.29 dna:scaffold     v1  0\n26      ADWL01015058.1    N   1067 47.14 dna:scaffold     v1  0\n27 Oglab04_unplaced014    N   1099 43.68 dna:scaffold     v1  0\n28      ADWL01009716.1    N   1200 50.08 dna:scaffold     v1  0\n29 Oglab04_unplaced051    N   1834 48.39 dna:scaffold     v1  0\n30      ADWL01025219.1    N   2000 54.35 dna:scaffold     v1  0\n<\/code><\/pre>\n<p><a name=\"cal\"><\/a><\/p>\n<h5>Calculating a sum - <code>sum(dataframe)<\/code> with filtering on an other column<\/h5>\n<pre><code>> sum(myGenomeSubset$Length)\n[1] 629495529\n\n> sum(myGenomeSubset$Length[myGenomeSubset$Type.1==&quot;v1&quot;])\n[1] 285037524\n\n> sum(myGenomeSubset$Length[myGenomeSubset$Type.1==&quot;v2&quot;])\n[1] 344458005\n<\/code><\/pre>\n<p><a name=\"length\"><\/a><\/p>\n<h5>Getting the number of elements in a dataframe - <code>length(dataframe)<\/code> with filtering on an other column<\/h5>\n<pre><code>> length(myGenomeSubset$Length[myGenomeSubset$Type.1==&quot;v1&quot;])\n[1] 1939\n\n> sum(myGenomeSubset$Length[myGenomeSubset$Type.1==&quot;v1&quot;])\n[1] 31382050\n\n> length(myGenomeSubset$Length[myGenomeSubset$Type.1==&quot;v2&quot;])\n[1] 47\n\n> sum(myGenomeSubset$Length[myGenomeSubset$Type.1==&quot;v2&quot;])\n[1] 2863041\n<\/code><\/pre>\n<p><a name=\"order\"><\/a><\/p>\n<h5>Ordering dataframe on one column<\/h5>\n<pre><code>myGenomeOrdered &lt;- myGenomeSubset[order(myGenomeSubset$Name),]\n\n> head(myGenomeOrdered)\n    Name Type   Length  X.GC       Organism Type.1 mb\n11 Chr01    N 32613412 43.53 dna:chromosome     v1 32\n13 Chr01    N 39656875 43.05 dna:chromosome     v2 39\n10 Chr02    N 29142869 43.19 dna:chromosome     v1 29\n14 Chr02    N 34451706 42.81 dna:chromosome     v2 34\n12 Chr03    N 33053699 43.20 dna:chromosome     v1 33\n15 Chr03    N 35526804 43.23 dna:chromosome     v2 35<\/code><\/pre>\n<p><a name=\"summary\"><\/a><\/p>\n<h5>Getting summaries of values of a column  - <code>summary<\/code><\/h5>\n<pre><code>> summary(mysSaffSubset$Length)\n   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. \n   1026    3214    5613   17243   12601 1478587 <\/code><\/pre>\n<hr \/>\n<p><a name=\"plot\"><\/a><\/p>\n<h3>Plotting data from a dataframe with <code>ggplot<\/code> library<\/h3>\n<p>To build a plot, the same following basic template can be used for several plot types :<\/p>\n<p><code>ggplot(data = &lt;DATA&gt;, aes = (&lt;MAPPINGS&gt;)) +  &lt;GEOM_FUNCTION&gt;()<\/code><\/p>\n<ul>\n<li>use the ggplot() function and bind the plot to a specific data frame using the <code>data<\/code> argument<\/li>\n<li>use the <code>aes<\/code> function to select the variables to be plotted and to define how tu present them in the graph (e.g. x\/y positions, size, shape, color)<\/li>\n<li>add \u2018geoms\u2019 \u2013 graphical representations of the data in the plot (points, lines, bars) such as <code>geom_point()<\/code>, <code>geom_boxplot()<\/code>,<code>geom_line()<\/code>, <code>geom-bar()<\/code><\/li>\n<\/ul>\n<p><a name=\"head\"><\/a><\/p>\n<h3>with <code>ggplot()<\/code>  + <code>geom_bar(stat = &quot;identity&quot;)<\/code>]<\/h3>\n<p>ggplot is a plotting package that makes simple to create complex plots from data stored in a data frame. It provides a programmatic interface for specifying what variables to plot, how they are displayed, and general visual properties.<\/p>\n<p><a href=\"https:\/\/datacarpentry.org\/r-socialsci\/04-ggplot2\/\">https:\/\/datacarpentry.org\/r-socialsci\/04-ggplot2\/<\/a><\/p>\n<p><a name=\"barplot\"><\/a><\/p>\n<h5>Creating a barplot with <code>geom_bar(stat = &quot;identity&quot;)<\/code>]<\/h5>\n<p>Barplots are useful for visualizing categorical data. By default, geom_bar accepts a variable for x, and plots the number of instances each value of x (in this case, chromosome) appears in the dataset.<\/p>\n<p>Here, we will :<\/p>\n<ul>\n<li>plot the size (mb) of each chromosome from each genome version with geom_bar<\/li>\n<li>use the fill aesthetic for the geom_bar() geom to color bars by the size of each chromosome for each genome version<\/li>\n<li>By default, geom_bar uses stat=&quot;bin&quot; to make the height of each bar equal to the number of cases in each group (it is incompatible with mapping values to the y aesthetic). Here we use <code>stat=&quot;identity&quot;<\/code> because we want the heights of the bars to represent values in the data (with a y aesthetic).<\/li>\n<\/ul>\n<p><a href=\"http:\/\/www.sthda.com\/french\/wiki\/ggplot2-barplots-guide-de-demarrage-rapide-logiciel-r-et-visualisation-de-donnees#barplots-basiques\">http:\/\/www.sthda.com\/french\/wiki\/ggplot2-barplots-guide-de-demarrage-rapide-logiciel-r-et-visualisation-de-donnees#barplots-basiques<\/a><\/p>\n<p><img decoding=\"async\" class=\"img-responsive\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/R\/barplot-type.png\" alt=\"barplot\" \/><\/p>\n<pre><code>#basic barplot\np &lt;- ggplot(data = myGenomeSubset, aes(x = Name, y=mb, fill=Type.1)) + \n      geom_bar(stat = &quot;identity&quot;)\np <\/code><\/pre>\n<p><a name=\"dodge\"><\/a><\/p>\n<h5>distinct plot - <code>position=position_dodge()<\/code> and flip plot with <code>coord_flip()<\/code><\/h5>\n<ul>\n<li>\n<p>We can separate the portions of the stacked bar that correspond to each genome version and put them side-by-side by using the position argument for geom_bar() and setting it to \u201cdodge\u201d.<\/p>\n<\/li>\n<li>\n<p><code>coord_flip()<\/code>: Flip cartesian coordinates so that horizontal becomes vertical, and vertical, horizontal<\/p>\n<\/li>\n<\/ul>\n<p><img decoding=\"async\" class=\"img-responsive\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/R\/barplot-flip.png\" alt=\"barplot\" \/><\/p>\n<pre><code>#basic barplot\nq &lt;- ggplot(data = myGenomeSubset, aes(x = Name, y=mb, fill=Type.1)) + \n      geom_bar(stat = &quot;identity&quot;, position=position_dodge())\n#horizontal\nq + coord_flip()<\/code><\/pre>\n<p><a name=\"save\"><\/a><\/p>\n<h5>save into a file<\/h5>\n<pre><code>jpeg(file=&quot;pseudomolOMAP.jpg&quot;);\n#basic barplot\nq &lt;- ggplot(data = myGenomeSubset, aes(x = Name, y=mb, fill=Type.1)) + \n      geom_bar(stat = &quot;identity&quot;, position=position_dodge())\n#horizontal\nq + coord_flip()\ndev.off;<\/code><\/pre>\n<hr \/>\n<p><a name=\"count\"><\/a><\/p>\n<h5>Creating a barplot with <code>geom_bar(stat = &quot;count&quot;)<\/code>]<\/h5>\n<ul>\n<li>we use <code>stat=&quot;count&quot;<\/code> to make the height of each bar equal to the count of lines<\/li>\n<li>Adding Labels and Titles with <code>ylab(&lt;Y-LABEL&gt;)<\/code>, <code>xlab(&lt;X-LABEL&gt;)<\/code> , <code>ggtitle(&lt;TITLE-LABEL&gt;)<\/code><br \/>\n<img decoding=\"async\" class=\"img-responsive\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/R\/barplot-count.png\" alt=\"barplot\" \/><\/li>\n<\/ul>\n<pre><code>p &lt;- ggplot(myscaffSubset, aes(x=Type.1)) + geom_bar(stat=&quot;count&quot;, width=0.4, fill=&quot;steelblue&quot;) +\n    xlab(&quot;Genome version&quot;) +\n    ylab(&quot;Scaffold number&quot;) +\n    ggtitle(&quot;Number of scaffold per genome version&quot;)\np<\/code><\/pre>\n<hr \/>\n<p><a name=\"violinPlot\"><\/a><\/p>\n<h5>Plotting a violin plot  - <code>geom_violin()<\/code><\/h5>\n<ul>\n<li>Create a violin plot<\/li>\n<\/ul>\n<p><img decoding=\"async\" class=\"img-responsive\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/R\/violinPlot.png\" alt=\"barplot\" \/><\/p>\n<pre><code>p &lt;- ggplot(myScaffSubset, aes(x=Type.1, y=Length, color=Type.1)) + \n+   geom_violin(trim=TRUE) + stat_summary(fun.y=median, geom=&quot;point&quot;, size=2, color=&quot;red&quot;)\n> p<\/code><\/pre>\n<ul>\n<li>Save plot into a file\n<pre><code>\n> jpeg(file=&quot;scaffoldOMAP.jpg&quot;);\n> p &lt;- ggplot(myScaffSubset, aes(x=Type.1, y=Length, color=Type.1)) + <\/code><\/pre>\n<\/li>\n<li>geom_violin(trim=TRUE) + stat_summary(fun.y=median, geom=&quot;point&quot;, size=2, color=&quot;red&quot;)<br \/>\n<blockquote>\n<p>p<br \/>\ndev.off;<\/p>\n<pre><code><\/code><\/pre>\n<\/blockquote>\n<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"head\"><\/a><\/p>\n<h5>Arranging plots in a grid - <code>grid.arrange()<\/code><\/h5>\n<p><img decoding=\"async\" class=\"img-responsive\" width=\"100%\" src=\"https:\/\/southgreenplatform.github.io\/tutorials\/\/images\/R\/gridPlot.png\" alt=\"grid\" \/> <\/p>\n<pre><code>\nmyplot1 &lt;- ggplot(data = myGenomeSubset, aes(x = Name, y=mb, fill=Type.1)) + \n      geom_bar(stat = &quot;identity&quot;, position=position_dodge()) + coord_flip()\n\nmyplot2 &lt;- ggplot(myScaffSubset, aes(x=Type.1, y=Length, color=Type.1)) + \n  geom_violin(trim=TRUE) + stat_summary(fun.y=median, geom=&quot;point&quot;, size=2, color=&quot;red&quot;)\n\ngrid.arrange(myplot1, myplot2, ncol=2)\n<\/code><\/pre>\n<hr \/>\n<p><a name=\"print\"><\/a><\/p>\n<h3>Displaying and manipulating the dataframe content<\/h3>\n<p><a name=\"head\"><\/a><\/p>\n<h5>Printing the first lines - <code>head(dataframe)<\/code><\/h5>\n<hr \/>\n<h3>License<\/h3>\n<p><a name=\"license\"><\/a><\/p>\n<div>\nThe resource material is licensed under the Creative Commons Attribution 4.0 International License (<a href=\"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">here<\/a>).<br \/>\n<center><img decoding=\"async\" width=\"25%\" class=\"img-responsive\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\"\/><br \/>\n<\/center>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>R tutorial Description A step by step guide to start on R Authors christine Tranchant-Dubreuil (christine.tranchant@ird.fr) Creation Date 21\/09\/2018 Last&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/r-survival-manual\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":1325,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-483","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.2 - 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