plotP from SPIA

Question

[bojkem91]

Hi! I have a problem with plotP function from SPIA, it is constantly throwing me this error:

Error in text.default(-log(ph)[oks] + 0.7, -log(pb)[oks], labels = as.vector(x$ID)[oks],  : 
  zero-length 'labels' specified

This is my chunk of code for R markdown:

makeSPIAdata( 
  kgml.path = "kegg_data_1",
  organism = "hsa",
  out.path = "kegg_data_1"
)

# ENTREZIDs of DEGs
deg_entrezids2 <- res_dex_shrink2[deg_filter2, "ENTREZID"]
# Vector of LFCs of DEGs. Names are ENTREZIDs.
entrez_lfc_deg2 <- entrez_lfc2[deg_entrezids2]
entrez_lfc_deg2 <- entrez_lfc_deg2[order(entrez_lfc_deg2, decreasing = TRUE)]
head(entrez_lfc_deg2)

spia_results2 <- spia(
  de = entrez_lfc_deg2,
  all = res_dex_shrink2$ENTREZID,
  organism = "hsa",
  data.dir = "kegg_data_1/"
)
spia_results2

Two-evidence plot:
plotP(spia_results2, threshold = 0.63)


# Viewing data in KEGG ############################

pathview(
  # LFC to color pathway.
  gene.data = entrez_lfc_deg2,
  # We use top pathway by ES from GSEA.
  pathway.id = gsea_kegg_results2$ID[1],
  species = "hsa",
  # Coloring range <min LFC; max LFC>
  limit = list(gene = max(abs(entrez_lfc_deg2)), cpd = 1),
  kegg.dir = "kegg_data_1/"#kegg_data
)

And pathview is not executed.