emapplot 'x' must be an array of at least two dimensions

[asmariyaz23]

Hello,

I am trying to use emapplot and get the following error:

emapplot(GO_CC_down) + labs(title="Enrichment map for GO CC down") + theme(plot.title=element_text(hjust=0.5,size=15,face="bold"))

Error in rowSums(data[, cols]) : 
  'x' must be an array of at least two dimensions

Here is the object:

> GO_CC_down
#
# Result of Comparing 5 gene clusters 
#
#.. @fun 	 enrichGO 
#.. @geneClusters 	List of 5
 $ conc_0.1uM : chr(0) 
 $ conc_1uM   : chr "RNVU1-29"
 $ conc_10uM  : chr(0) 
 $ conc_100uM : chr [1:56] "HECW1" "PDK2" "MRC2" "VCAN" ...
 $ conc_1000uM: chr [1:21] "NKAIN4" "SLC2A9" "CDH6" "CEP70" ...
#...Result 	'data.frame':	3 obs. of  13 variables:
 $ Cluster       : Factor w/ 5 levels "conc_0.1uM","conc_1uM",..: 4 4 4
 $ ID            : chr  "GO:0016323" "GO:0009925" "GO:0045178"
 $ Description   : chr  "basolateral plasma membrane" "basal plasma membrane" "basal part of cell"
 $ GeneRatio     : chr  "5/46" "5/46" "5/46"
 $ BgRatio       : chr  "264/19960" "298/19960" "317/19960"
 $ RichFactor    : num  0.0189 0.0168 0.0158
 $ FoldEnrichment: num  8.22 7.28 6.84
 $ zScore        : num  5.67 5.25 5.04
 $ pvalue        : num  0.000343 0.000596 0.000787
 $ p.adjust      : num  0.0268 0.0268 0.0268
 $ qvalue        : num  0.0226 0.0226 0.0226
 $ geneID        : chr  "ABCC3/SLC2A9/SLC7A7/AQP3/SLCO2A1" "ABCC3/SLC2A9/SLC7A7/AQP3/SLCO2A1" "ABCC3/SLC2A9/SLC7A7/AQP3/SLCO2A1"
 $ Count         : int  5 5 5
#.. number of enriched terms found for each gene cluster:
#..   conc_0.1uM: 0 
#..   conc_1uM: 0 
#..   conc_10uM: 0 
#..   conc_100uM: 3 
#..   conc_1000uM: 0 

Could you help me understand why I am getting this error?

Thank you,
Asma

[guidohooiveld]

Using the included example data your code is working for me; be sure to also explicitly load the library(ggplot2)!
Also not that most of your clusters are empty! Thus no enriched terms.

>
> ## just to be sure;  install GitHub version of enrichplot
> ## since some issues with emapplot were recently fixed
>
> BiocManager::install(c('YuLab-SMU/enrichplot'), force=TRUE)
> # <<snip>>
>
> library(clusterProfiler)
> library(enrichplot)
> library(org.Hs.eg.db)
> 
> data(gcSample)
>
> all_genes_GO_MF <- compareCluster(geneCluster = gcSample, 
+                                   fun = enrichGO,
+                                   ont = "MF",
+                                   OrgDb ="org.Hs.eg.db",
+                                   pAdjustMethod = "BH",
+                                   keyType = "ENTREZID",
+                                   pvalueCutoff  = 0.05,
+                                   qvalueCutoff  = 0.05,
+                                   minGSSize = 10,
+                                   maxGSSize = 500,
+                                   readable=TRUE)
>  
> all_genes_GO_MF_sim <- pairwise_termsim(all_genes_GO_MF) 
> 
> all_genes_GO_MF
#
# Result of Comparing 8 gene clusters 
#
#.. @fun         enrichGO 
#.. @geneClusters       List of 8
 $ X1: chr [1:216] "4597" "7111" "5266" "2175" ...
 $ X2: chr [1:805] "23450" "5160" "7126" "26118" ...
 $ X3: chr [1:392] "894" "7057" "22906" "3339" ...
 $ X4: chr [1:838] "5573" "7453" "5245" "23450" ...
 $ X5: chr [1:929] "5982" "7318" "6352" "2101" ...
 $ X6: chr [1:585] "5337" "9295" "4035" "811" ...
 $ X7: chr [1:582] "2621" "2665" "5690" "3608" ...
 $ X8: chr [1:237] "2665" "4735" "1327" "3192" ...
#...Result      'data.frame':   108 obs. of  13 variables:
 $ Cluster       : Factor w/ 8 levels "X1","X2","X3",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ ID            : chr  "GO:0003680" "GO:1901681" "GO:1902282" "GO:0140375" ...
 $ Description   : chr  "minor groove of adenine-thymine-rich DNA binding" "sulfur compound binding" "voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization" "immune receptor activity" ...
 $ GeneRatio     : chr  "3/204" "11/204" "3/204" "8/204" ...
 $ BgRatio       : chr  "10/18737" "277/18737" "12/18737" "154/18737" ...
 $ RichFactor    : num  0.3 0.0397 0.25 0.0519 0.0598 ...
 $ FoldEnrichment: num  27.55 3.65 22.96 4.77 5.5 ...
 $ zScore        : num  8.81 4.66 7.98 4.93 5.12 ...
 $ pvalue        : num  0.000144 0.000237 0.00026 0.000289 0.000295 ...
 $ p.adjust      : num  0.0278 0.0278 0.0278 0.0278 0.0278 ...
 $ qvalue        : num  0.0254 0.0254 0.0254 0.0254 0.0254 ...
 $ geneID        : chr  "PAX6/HMGA1/HAND2" "ENPP1/KNG1/COLQ/H1-1/APLP1/NRTN/NRP2/CXCL8/POSTN/PLA2G2D/PNPLA3" "KCNH2/KCND3/KCNE5" "IL1R2/GPR17/IL2RA/FCER2/IL12RB2/NCR3/CXCR6/GFRA3" ...
 $ Count         : int  3 11 3 8 7 10 3 6 8 3 ...
#.. number of enriched terms found for each gene cluster:
#..   X1: 10 
#..   X2: 1 
#..   X3: 0 
#..   X4: 11 
#..   X5: 7 
#..   X6: 0 
#..   X7: 40 
#..   X8: 39 
#
#...Citation
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, 
W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. 
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. 
The Innovation. 2021, 2(3):100141 

>
>
> library(ggplot2)
> 
> emapplot(all_genes_GO_MF_sim, pie="Count", size_edge = 1.5, showCategory = 4) + 
+    labs(title="Enrichment map for GO MF text") +
+    theme( plot.title=element_text(hjust=0.5, size=15, face="bold") )
Coordinate system already present. Adding new coordinate system, which will
replace the existing one.
>