Lint R files

bioinfodlsu · May 4, 2023 · d43aa1d · d43aa1d
1 parent 35a5fec
commit d43aa1d
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Showing 3 changed files with 29 additions and 21 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -3,6 +3,10 @@
 		"editor.defaultFormatter": "ms-python.autopep8",
 		"editor.formatOnSave": true
 	},
+	"[r]": {
+		"editor.defaultFormatter": "REditorSupport.r",
+		"editor.formatOnSave": true
+	},
 	"python.formatting.provider": "none",
 	"editor.codeActionsOnSave": {
 		"source.organizeImports": true

diff --git a/enrichment_analysis/kegg-enrichment.r b/enrichment_analysis/kegg-enrichment.r
@@ -12,7 +12,7 @@ background <- background[[1]]
 genes_transcript <- c()
 na_genes_transcript <- c()
 for (gene in genes) {
-  transcript_id <- RiceIDConvert(gene, fromType = 'MSU', toType = 'TRANSCRIPTID')
+  transcript_id <- RiceIDConvert(gene, fromType = "MSU", toType = "TRANSCRIPTID")
   for (id in transcript_id$TRANSCRIPTID) {
     if (is.na(id)) {
       print(gene)
@@ -23,13 +23,13 @@ for (gene in genes) {
   }
 }
 
-lapply(na_genes_transcript, write, 'data/cluster1-na-transcript-id.txt', append = T, sep = '\n')
-lapply(genes_transcript, write, 'data/cluster1-transcript-id.txt', append = T, sep = '\n')
+lapply(na_genes_transcript, write, "data/cluster1-na-transcript-id.txt", append = TRUE, sep = "\n")
+lapply(genes_transcript, write, "data/cluster1-transcript-id.txt", append = TRUE, sep = "\n")
 
 background_transcript <- c()
 na_background_transcript <- c()
 for (gene in background) {
-  transcript_id <- RiceIDConvert(gene, fromType = 'MSU', toType = 'TRANSCRIPTID')
+  transcript_id <- RiceIDConvert(gene, fromType = "MSU", toType = "TRANSCRIPTID")
   for (id in transcript_id$TRANSCRIPTID) {
     if (is.na(id)) {
       print(gene)
@@ -40,21 +40,25 @@ for (gene in background) {
   }
 }
 
-lapply(na_background_transcript, write, 'data/all-na-transcript-id.txt', append = T, sep = '\n')
-lapply(background_transcript, write, 'data/all-transcript-id.txt', append = T, sep = '\n')
+lapply(na_background_transcript, write, "data/all-na-transcript-id.txt", append = TRUE, sep = "\n")
+lapply(background_transcript, write, "data/all-transcript-id.txt", append = TRUE, sep = "\n")
 
-kegg <- enrichKEGG(gene = genes_transcript, 
-                   universe = background_transcript, 
-                   organism = "dosa", 
-                   keyType = "kegg", 
+kegg <- enrichKEGG(
+  gene = genes_transcript,
+  universe = background_transcript,
+  organism = "dosa",
+  keyType = "kegg",
 )
 
 kegg_df <- as.data.frame(kegg)
-write.table(kegg_df, "data/kegg_df.txt",  sep="\t", row.names=FALSE, quote=FALSE)
+write.table(kegg_df, "data/kegg_df.txt", sep = "\t", row.names = FALSE, quote = FALSE)
 
-p1 <- dotplot(kegg, showCategory = nrow(kegg_df),
-              title = "Top 10 most statistically significant enriched KEGG terms",
-              font.size = 10)
+p1 <- dotplot(kegg,
+  showCategory = nrow(kegg_df),
+  title = "Top 10 most statistically significant enriched KEGG terms",
+  font.size = 10
+)
 ggsave(p1,
-       filename = "data/kegg_dotplot.png",
-       height = 22,width = 22,units = "cm") 
+  filename = "data/kegg_dotplot.png",
+  height = 22, width = 22, units = "cm"
+)
diff --git a/enrichment_analysis/msu-to-transcript-id.r b/enrichment_analysis/msu-to-transcript-id.r
@@ -8,10 +8,10 @@ all_transcript <- c()
 na_all_transcript <- c()
 
 for (gene in all_genes) {
-  transcript_id <- RiceIDConvert(gene, fromType = 'MSU', toType = 'TRANSCRIPTID')
+  transcript_id <- RiceIDConvert(gene, fromType = "MSU", toType = "TRANSCRIPTID")
   transcript_id_list <- c()
   transcript_id_list <- append(transcript_id_list, gene)
-  
+
   for (id in transcript_id$TRANSCRIPTID) {
     if (is.na(id)) {
       print(gene)
@@ -20,9 +20,9 @@ for (gene in all_genes) {
       transcript_id_list <- append(transcript_id_list, id)
     }
   }
-  
+
   all_transcript <- append(all_transcript, list(transcript_id_list))
 }
 
-lapply(na_all_transcript, write, 'data/temp/all-na-transcript-id.txt', append = T, sep = '\n')
-lapply(all_transcript, write, 'data/temp/all-transcript-id.txt', append = T, sep = '\n')
+lapply(na_all_transcript, write, "data/temp/all-na-transcript-id.txt", append = TRUE, sep = "\n")
+lapply(all_transcript, write, "data/temp/all-transcript-id.txt", append = TRUE, sep = "\n")