R Script For Extract Levels
Dear B, I got error with heat map in R i want a R function to extract taxonomy levels in otu table as follows
extract.name.level = function(x, level){
a=c(unlist(strsplit(x,';')),'Other')
paste(a[1:min(level,length(a))],collapse=';')
}
OTU table
OTU ID Control P1 S1 taxonomy
3506234 1298 466 1074 Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae; Proteiniphilum
New.ReferenceOTU31 731 0 2 Bacteria; Bacteroidetes; Sphingobacteria; Sphingobacteriales
4444585 700 374 520 Bacteria
New.CleanUp.ReferenceOTU1531 606 84 26 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae; Tetrathiobacter
670013 441 17 172 Bacteria; Synergistetes; Synergistia; Synergistales; Synergistaceae
661526 405 90 49 Bacteria; Synergistetes; Synergistia; Synergistales; Synergistaceae; Cloacibacillus
4367900 374 103 556 Bacteria; Tenericutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Acholeplasma
817135 358 30 206 Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Desulfovibrio
Thank you
Seba
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Judging from your function, are you trying to extract rows of that table having a given string in the taxonomy field or something else? Perhaps you also just want to know what levels there are, which would be something like:
What's your problem precisely? The function seems to work and extract the first n levels separated by ';' if x is a character vector of length 1:
Not sure what the "Other" is for, doesn't make much sense to me to have this.
How is that connected to heatmaps?
If I understand it correctly you mean to use the taxonomy columns as row names for your heatmap and the three columns in the middle as the heatmap itself Is it correct?
Do you need only the last taxonomy ID to be extracted?
Thank you for quick response... Yes i followed the tutorial to make heatmap but got error with taxa Id in the heatmap http://learningomics.wordpress.com/
It produced heatmap without taxa id