Entering edit mode
5.9 years ago
gowthamee
•
0
When using GOplot to create the the visualizations, I have the following errors.
I generated the data (circ_final) using the function circle_dat. The resulting data frame looks the same as the example (circ) shown in the vignette - http://wencke.github.io, with one change. My data doesn't have a column for ID, the vignette states that the column ID is optional.
Now when I use the data (circ_final), with the function GOBar
GOBar(subset(circ_final, category == "KEGG_2016"))
I get the following error
Error in tapply(X = X, INDEX = x, FUN = FUN, ...) :
arguments must have same length
with the function GOBubble,
GOBubble(circ_final, ID = F)
I get the following error
Error in data.frame(fg_params, label = as.vector(label_matrix), stringsAsFactors = FALSE) :
arguments imply differing number of rows: 1, 0
with the function GOChord,
GOChord(circ_chord, space = 0.02, gene.order = "logFC", gene.space = 0.25, gene.size = 5)
I get the following error
Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [2] is duplicated
In addition: Warning messages:
1: In min(df_genes$logFC) : no non-missing arguments to min; returning Inf
2: In max(df_genes$logFC) :
no non-missing arguments to max; returning -Inf
3: In min(df_genes$logFC) : no non-missing arguments to min; returning Inf
4: In max(df_genes$logFC) :
no non-missing arguments to max; returning -Inf
However, I can reproduce the plots shown in the vignette, without any problem. If anyone has any idea how to solve these errors, please help.
The output of the function circle_dat for my data is the object circ_final, and looks like the output of the object circ in vignette, but without the column "ID"
----------
- category; term; count; genes; logFC; adj_pval; zscore
1;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;ACOT8;-0.158035734268892;0.002167;-0.534522483824849
2;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;IDH1;0.120796971790904;0.002167;-0.534522483824849
3;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;CROT;-0.0847676760334766;0.002167;-0.534522483824849
4;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;ALDH3A2;0.052720360624293;0.002167;-0.534522483824849
5;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;SLC25A17;0.153694087053354;0.002167;-0.534522483824849
6;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;AMACR;-0.151430954021018;0.002167;-0.534522483824849
7;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;ACOX2;0.103125835296529;0.002167;-0.534522483824849
8;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;NUDT19;-0.337277779520686;0.002167;-0.534522483824849
9;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;HACL1;-0.0649767165519108;0.002167;-0.534522483824849
10;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;ACOX3;0.0668166932889731;0.002167;-0.534522483824849
11;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;ACAA1;-0.0127540536397781;0.002167;-0.534522483824849
12;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;CRAT;-0.162788379212945;0.002167;-0.534522483824849
13;Reactome_2016;Peroxisomal lipid metabolism_Homo;14;SLC27A2;-0.770127494414573;0.002167;-0.534522483824849
14;Reactome_2016;Peroxisomal lipid metabolism_Homo ;14;ABCD1;0.0668089719575997;0.002167;-0.534522483824849
15;KEGG_2016;Peroxisome_Homo ;29;ABCD4;-0.0834096142719645;0.002663;-2.04264871994757
16;KEGG_2016;Peroxisome_Homo ;29;ABCD3;-0.111481325106831;0.002663;-2.04264871994757
17;KEGG_2016;Peroxisome_Homo ;29;CROT;-0.0847676760334766;0.002663;-2.04264871994757
18;KEGG_2016;Peroxisome_Homo ;29;PMVK;-0.268425309689376;0.002663;-2.04264871994757
19;KEGG_2016;Peroxisome_Homo ;29;NUDT19;-0.337277779520686;0.002663;-2.04264871994757
20;KEGG_2016;Peroxisome_Homo ;29;HACL1;-0.0649767165519108;0.002663;-2.04264871994757
21;KEGG_2016;Peroxisome_Homo ;29;ACAA1;-0.0127540536397781;0.002663;-2.04264871994757
22;KEGG_2016;Peroxisome_Homo ;29;XDH;0.317121842677734;0.002663;-2.04264871994757
23;KEGG_2016;Peroxisome_Homo ;29;ABCD1;0.0668089719575997;0.002663;-2.04264871994757
24;KEGG_2016;Peroxisome_Homo ;29;NUDT12;0.186037612539135;0.002663;-2.04264871994757
25;KEGG_2016;Peroxisome_Homo ;29;ACOT8;-0.158035734268892;0.002663;-2.04264871994757
26;KEGG_2016;Peroxisome_Homo ;29;IDH1;0.120796971790904;0.002663;-2.04264871994757
27;KEGG_2016;Peroxisome_Homo ;29;ECH1;-0.125341014540492;0.002663;-2.04264871994757
28;KEGG_2016;Peroxisome_Homo ;29;IDH2;-0.165885616809657;0.002663;-2.04264871994757
29;KEGG_2016;Peroxisome_Homo ;29;ACSL4;0.130200139967999;0.002663;-2.04264871994757
30;KEGG_2016;Peroxisome_Homo ;29;PEX12;-0.153329055679451;0.002663;-2.04264871994757
31;KEGG_2016;Peroxisome_Homo ;29;SOD2;-0.141589849175332;0.002663;-2.04264871994757
32;KEGG_2016;Peroxisome_Homo ;29;SOD1;-0.550596702101043;0.002663;-2.04264871994757
33;KEGG_2016;Peroxisome_Homo ;29;PEX7;-0.363649517860036;0.002663;-2.04264871994757
34;KEGG_2016;Peroxisome_Homo ;29;SLC25A17;0.153694087053354;0.002663;-2.04264871994757
35;KEGG_2016;Peroxisome_Homo ;29;AMACR;-0.151430954021018;0.002663;-2.04264871994757
36;KEGG_2016;Peroxisome_Homo ;29;ACOX2;0.103125835296529;0.002663;-2.04264871994757
37;KEGG_2016;Peroxisome_Homo ;29;PEX6;0.212478952929781;0.002663;-2.04264871994757
38;KEGG_2016;Peroxisome_Homo ;29;PXMP2;-0.507664355573977;0.002663;-2.04264871994757
39;KEGG_2016;Peroxisome_Homo ;29;FAR1;-0.403641070520405;0.002663;-2.04264871994757
40;KEGG_2016;Peroxisome_Homo ;29;ACOX3;0.0668166932889731;0.002663;-2.04264871994757
41;KEGG_2016;Peroxisome_Homo ;29;PEX11G;-0.556947840846257;0.002663;-2.04264871994757
42;KEGG_2016;Peroxisome_Homo ;29;CRAT;-0.162788379212945;0.002663;-2.04264871994757
43;KEGG_2016;Peroxisome_Homo ;29;SLC27A2;-0.770127494414573;0.002663;-2.04264871994757
44;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;RB1;-0.187597813571551;0.03389;0.942809041582063
45;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;DUT;-0.324139414766579;0.03389;0.942809041582063
46;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;DUSP1;0.123162801083886;0.03389;0.942809041582063
47;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;CITED2;0.239989553330966;0.03389;0.942809041582063
48;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;NR2F1;0.210133798117667;0.03389;0.942809041582063
49;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;NR1H3;0.16115667057699;0.03389;0.942809041582063
50;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;RELA;0.239853852532915;0.03389;0.942809041582063
51;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;NFKBIA;0.346271757050777;0.03389;0.942809041582063
52;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;PRKAR1B;-0.494478218041094;0.03389;0.942809041582063
53;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;SP1;0.200895067389787;0.03389;0.942809041582063
54;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;PRKAR1A;-0.137596635029533;0.03389;0.942809041582063
55;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;PRKAR2B;-0.103877028165797;0.03389;0.942809041582063
56;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;MYC;0.821888293720954;0.03389;0.942809041582063
57;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;NRIP1;0.134567337510974;0.03389;0.942809041582063
58;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;ME1;0.201263740882296;0.03389;0.942809041582063
59;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;EP300;0.374651072864142;0.03389;0.942809041582063
60;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;PPARGC1A;-0.0307721456707295;0.03389;0.942809041582063
61;BioCarta_2016;Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa_Homo ;18;MAPK3;-0.109880652806064;0.03389;0.942809041582063
