Entering edit mode
4.3 years ago
bojkem91
•
0
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.