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