Hi! I am working with the species Atlantic salmon (sasa), and I have performed RNAseq on some tissues. I want to visualize the pathways sasa01040 - Biosynthesis of unsaturated fatty acids (number 85) and sasa01212 Fatty acid metabolism (89) using pathview, comparing two tissues with eachother. I have already visualized other pathways using this code, which has worked, and the figures are looking good. When putting in number 85 and 89, I get this error message as seen below. I have tried adjusting kegg.native = F and same.layer = F, but these figures are not usable.

Thank you in advance for tips how to get around this problem.

> for(i in 85) {
+   
+   pv.out<-pathview(gene.data = mat2c[,1],pathway.id = sasa_kegg_pw_2025[i,1],
+                    species = "sasa", out.suffix = sasa_kegg_pw_2025[i,2], kegg.native = T,
+                   low = list(gene = "blue"), mid = list(gene = "gray"),
+                    high = list(gene = "red"), na.col = "transparent",
+                    same.layer = T, limit = 3) 
+   print(pv.out)
+   
+   
+ }
Warning: No annotation package for the species sasa, gene symbols not mapped!
Info: Working in directory C:/Users/ingholml/OneDrive - Universitetet i Oslo/rnaseq_oct24/ncbi/kegg2
Info: Writing image file sasa01040.Biosynthesis of unsaturated fatty acids.png
Info: some node width is different from others, and hence adjusted!
Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : 
  negative length vectors are not allowed 

sessionInfo( )
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] C

time zone: Europe/Oslo
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pathview_1.40.0       clusterProfiler_4.8.3 ggpubr_0.6.0          ggplot2_3.5.1        
[5] AnnotationHub_3.8.0   BiocFileCache_2.8.0   dbplyr_2.3.4          BiocGenerics_0.46.0  

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3            rstudioapi_0.15.0             jsonlite_1.8.8               
  [4] magrittr_2.0.3                farver_2.1.1                  fs_1.6.3                     
  [7] zlibbioc_1.46.0               vctrs_0.6.5                   memoise_2.0.1                
 [10] RCurl_1.98-1.14               ggtree_3.8.2                  rstatix_0.7.2                
 [13] htmltools_0.5.7               S4Arrays_1.0.5                curl_6.0.1                   
 [16] broom_1.0.5                   gridGraphics_0.5-1            plyr_1.8.9                   
 [19] cachem_1.0.8                  igraph_2.1.2                  mime_0.12                    
 [22] lifecycle_1.0.4               pkgconfig_2.0.3               Matrix_1.6-5                 
 [25] R6_2.5.1                      fastmap_1.1.1                 gson_0.1.0                   
 [28] shiny_1.8.0                   GenomeInfoDbData_1.2.10       MatrixGenerics_1.12.3        
 [31] digest_0.6.34                 aplot_0.2.4                   enrichplot_1.20.3            
 [34] colorspace_2.1-0              patchwork_1.2.0               AnnotationDbi_1.62.2         
 [37] S4Vectors_0.38.1              DESeq2_1.40.2                 GenomicRanges_1.52.0         
 [40] RSQLite_2.3.4                 org.Hs.eg.db_3.17.0           filelock_1.0.3               
 [43] fansi_1.0.6                   httr_1.4.7                    polyclip_1.10-6              
 [46] abind_1.4-5                   compiler_4.3.2                bit64_4.0.5                  
 [49] withr_2.5.2                   downloader_0.4                backports_1.4.1              
 [52] BiocParallel_1.34.2           carData_3.0-5                 viridis_0.6.4                
 [55] DBI_1.2.1                     ggforce_0.4.1                 ggsignif_0.6.4               
 [58] MASS_7.3-60.0.1               rappdirs_0.3.3                DelayedArray_0.26.7          
 [61] HDO.db_0.99.1                 tools_4.3.2                   interactiveDisplayBase_1.38.0
 [64] ape_5.7-1                     scatterpie_0.2.4              httpuv_1.6.13                
 [67] glue_1.7.0                    promises_1.2.1                nlme_3.1-163                 
 [70] GOSemSim_2.26.1               grid_4.3.2                    shadowtext_0.1.4             
 [73] reshape2_1.4.4                fgsea_1.26.0                  generics_0.1.3               
 [76] gtable_0.3.4                  tidyr_1.3.1                   data.table_1.14.10           
 [79] tidygraph_1.3.1               car_3.1-2                     utf8_1.2.4                   
 [82] XVector_0.40.0                BiocVersion_3.17.1            ggrepel_0.9.5                
 [85] pillar_1.9.0                  stringr_1.5.1                 yulab.utils_0.1.9            
 [88] later_1.3.2                   splines_4.3.2                 dplyr_1.1.4                  
 [91] tweenr_2.0.2                  treeio_1.24.3                 lattice_0.22-5               
 [94] bit_4.0.5                     tidyselect_1.2.0              GO.db_3.17.0                 
 [97] locfit_1.5-9.8                Biostrings_2.68.1             gridExtra_2.3                
[100] IRanges_2.34.1                SummarizedExperiment_1.30.2   stats4_4.3.2                 
[103] graphlayouts_1.2.1            Biobase_2.60.0                matrixStats_1.2.0            
[106] KEGGgraph_1.60.0              stringi_1.8.3                 yaml_2.3.8                   
[109] lazyeval_0.2.2                ggfun_0.1.8                   codetools_0.2-19             
[112] ggraph_2.2.1                  tibble_3.2.1                  qvalue_2.32.0                
[115] Rgraphviz_2.44.0              graph_1.78.0                  BiocManager_1.30.25          
[118] ggplotify_0.1.2               cli_3.6.2                     xtable_1.8-4                 
[121] munsell_0.5.0                 Rcpp_1.0.12                   GenomeInfoDb_1.36.4          
[124] png_0.1-8                     XML_3.99-0.16                 parallel_4.3.2               
[127] ellipsis_0.3.2                blob_1.2.4                    DOSE_3.26.2                  
[130] bitops_1.0-7                  viridisLite_0.4.2             tidytree_0.4.6               
[133] scales_1.3.0                  purrr_1.0.2                   crayon_1.5.2                 
[136] rlang_1.1.3                   cowplot_1.1.2                 fastmatch_1.1-4              
[139] KEGGREST_1.40.1