R之cast公式使用

cast用来替代透视表简直完美。我们有一个33列的数据表，数据保存在Dmean和Rmean中

> colnames(tmp)
 [1] "ORF"                    "Dmean"                  "Rmean"
 [4] "seed_eggNOG_ortholog"   "seed_ortholog_evalue"   "seed_ortholog_score"
 [7] "best_tax_level"         "Preferred_name"         "GOs"
[10] "EC"                     "KEGG_ko"                "KEGG_Pathway"
[13] "KEGG_Module"            "KEGG_Reaction"          "KEGG_rclass"
[16] "BRITE"                  "KEGG_TC"                "CAZy"
[19] "BiGG_Reaction"          "taxonomic scope"        "eggNOG OGs"
[22] "best eggNOG OG"         "COG Functional cat."    "eggNOG free text desc."
[25] "gene name"              "mag"                    "d"
[28] "p"                      "c"                      "o"
[31] "type"                   "function"               "redox"

我们看下按照4种redox的平均值，行放在~的左边，列放在右边，值放在value.var中。本例中我们没有放列用.即可

> dcast(tmp,redox~.,mean,value.var = c("Dmean","Rmean"))
       redox      Dmean     Rmean
1:      <NA> 0.10999522 0.1059578
2:         0 0.07981577 0.2133641
3: oxidizing 0.21655478 0.5128236
4:  reducing 0.27810043 2.5835617

有一个变量比较特殊，function，这个变量在系统中会默认为是函数，用的时候要用反引号括起来（就是esc键下面的那个）

dcast(tmp,type+`function`+redox~.,sum,value.var = c("Dmean","Rmean"))
                              type               function     redox
 1:                           <NA>                   <NA>      <NA>
 2: Redox cofactors reduce/oxidize  Acetyl-CoA production  reducing
 3: Redox cofactors reduce/oxidize       Acrylate pathway oxidizing
 4: Redox cofactors reduce/oxidize    Butyrate production oxidizing
 5: Redox cofactors reduce/oxidize  Formate dehydrogenase  reducing
 6: Redox cofactors reduce/oxidize             Glycolysis  reducing
 7: Redox cofactors reduce/oxidize         Methanogenesis oxidizing
 8: Redox cofactors reduce/oxidize      Nitrite reduction oxidizing
 9: Redox cofactors reduce/oxidize      Nitrogen fixation oxidizing
10: Redox cofactors reduce/oxidize      Succinate pathway oxidizing
11: Redox cofactors reduce/oxidize      Sulfate reduction oxidizing
12: Redox cofactors reduce/oxidize Wood-Ljungdahl pathway  reducing
13:                    hydrogenase            Bifurcating         0
14:                    hydrogenase      Energy-converting         0
15:                    hydrogenase           Fermentative         0
16:                    hydrogenase         Methanogenesis         0
17:                    hydrogenase            Respiratory         0
18:                    hydrogenase                Sensory         0
           Dmean        Rmean
 1: 885635.51860 8.531278e+05
 2:   1486.50772 1.806910e+03
 3:     48.97481 2.274363e+01
 4:    191.23024 4.386971e+02
 5:    167.65026 1.236114e+02
 6:   2129.58254 3.383825e+04
 7:     14.19904 1.838745e+02
 8:    176.11628 1.630629e+01
 9:     76.21357 2.316838e+00
10:   3405.19194 9.145290e+03
11:    251.55641 5.031805e+01
12:     67.11611 5.808091e+00
13:    268.67952 9.729305e+02
14:     43.62233 7.332491e+00
15:     47.23687 1.091006e+01
16:     13.83782 9.715857e+01
17:     17.29643 1.502281e+00
18:     17.90397 2.376741e+00