Dear all,
When I was trying to make a stacked bar plot using group.abundance in RAM, it
comes out the following error:
> group.abundance(data=list(data=data), rank="o",
+ top=NULL, count=FALSE, drop.unclassified=TRUE,
+ main="", file=NULL, ext=NULL,
+ height=8, width=16, bw=FALSE, ggplot=TRUE)
Error in FUN(X[[i]], ...) : object 'Taxon' not found
But there is no error with the default data "ITS1" in the RAM package, I have
compared my dataset using str() with the "ITS1":
>str(data)
'data.frame':1252 obs. of 13 variables:
$ CL1 : int 211 41 584 105 0 9 50 69 123 325 ...
$ CL2 : int 220 31 297 163 0 44 176 53 328 447 ...
$ CL3 : int 310 62 641 90 0 15 45 126 217 304 ...
$ SL1 : int 101 310 241 728 7 1087 605 146 558 102 ...
$ SL2 : int 328 370 466 722 1 685 514 172 393 111 ...
$ SL3 : int 220 358 188 751 3 533 607 209 198 116 ...
$ GL1 : int 337 752 44 256 0 202 208 309 250 252 ...
$ GL2 : int 257 1387 72 247 8 380 473 224 350 250 ...
$ GL3 : int 345 1243 162 234 1 167 273 224 416 252 ...
$ DL1 : int 1054 154 637 99 72 3 1 711 3 127 ...
$ DL2 : int 1526 81 307 122 34 2 3 607 0 103 ...
$ DL3 : int 1073 50 429 65 3451 7 3 106 83 247 ...
$ taxonomy: chr
"k__Bacteria;p__Chloroflexi;c__Gitt-GS-136;Ambiguous_taxa;Ambiguous_taxa;Ambiguous_taxa;Ambiguous_taxa"
"k__Bacteria;p__Acidobacteria;c__Subgroup_6;o__uncultured_Acidobacteria_bacterium;f__uncultured_Acidobacteria_ba"|
__truncated__
"k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Micrococcales;f__Micrococcaceae;g__Pseudarthrobacter;Ambiguous_taxa"
"k__Bacteria;p__Acidobacteria;c__Subgroup_6" ...
> str(ITS1)
'data.frame':4704 obs. of 17 variables:
$ P1001.1M1 : int 90 1100 2700 90 62 379 1173 1297 355 2 ...
$ P1001.1M2 : int 35 566 1429 44 27 245 449 1074 202 16 ...
$ P1001.1M3 : int 124 1341 3141 126 209 516 1451 2338 270 17 ...
$ P1001.1M4 : int 11 144 404 13 10 89 221 235 31 4 ...
$ P1001.1M5 : int 157 291 494 56 15 1245 234 700 1680 212 ...
$ P1001.1M6 : int 81 181 228 26 6 724 156 413 1029 76 ...
$ P1001.1M7 : int 223 283 440 89 2 795 212 979 1661 152 ...
$ P1001.1M8 : int 185 214 272 85 20 872 141 997 1973 344 ...
$ P1001.1M9 : int 100 3191 256 55 2033 126 1359 798 158 863 ...
$ P1001.1M10: int 40 1137 52 9 1066 41 514 509 55 195 ...
$ P1001.1M11: int 96 2555 186 70 654 230 2287 401 46 5146 ...
$ P1001.1M12: int 65 2600 85 26 44 128 2158 252 11 2511 ...
$ P1001.1M13: int 71 868 33 13 8 303 382 165 191 14672 ...
$ P1001.1M14: int 53 630 15 22 8 190 368 115 143 9210 ...
$ P1001.1M15: int 73 609 13 5 4 475 310 88 116 25993 ...
$ P1001.1M16: int 109 618 23 27 1 369 322 174 99 23664 ...
$ taxonomy : chr "k__Fungi; p__Ascomycota; c__Dothideomycetes;
o__Pleosporales; f__Pleosporaceae; g__Epicoccum" "k__Fungi; p__Ascomycota;
c__Dothideomycetes; o__Pleosporales; f__Pleosporaceae; g__Alternaria"
"k__Fungi; p__Ascomycota; c__Dothideomycetes; o__Capnodiales;
f__Mycosphaerellaceae; g__Cladosporium" "k__Fungi; p__Ascomycota;
c__Dothideomycetes; o__Capnodiales; f__Mycosphaerellaceae; g__Cladosporium" ...
Has anyone any idea how to solve this error? Any help will be appreciated.
Thanks,
Jinbiao
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