[R-sig-eco] Error in FUN(X[[i]], ...) : object 'Taxon' not found

[Jinbiao Li]

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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