Question: Error when using GOBar, GOBubble, GOChord function from GOplot package
0
gravatar for gowthamee
29 days ago by
gowthamee0
gowthamee0 wrote:

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
rna-seq R • 125 views
ADD COMMENTlink modified 29 days ago by genomax62k • written 29 days ago by gowthamee0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 837 users visited in the last hour