updates

Author: noriakis

R/doL0.R

@@ -24,9 +24,11 @@ doL0 <- function(stana, species, cl=NULL, doFix=TRUE,
         qqcat("Using grouping from the slot\n")
         cl <- stana@cl
     }
-    if (target!="snps" & is.null(mat)){
+    if (target=="genes" & is.null(mat)){
         qqcat("If needed, please provide preprocessed matrix of genes to `mat`\n")
         filtDf <- stana@genes[[species]]
+    } else if (target=="ko") {
+    	filtDf <- stana@kos[[species]]
     } else if (target=="snps"){
         filtDf <- stana@snps[[species]]
         if (deleteZeroDepth) {

R/plotCirclize.R

@@ -72,6 +72,8 @@ plotCirclize <- function(stana, candSp, genomeId, include_gene=NULL,
       info$genome_id <- sapply(strsplit(row.names(info),"\\|"),"[",3)
     } else if (stana@type=="InStrain") {
       info$genome_id <- info$scaffold
+    } else {
+      cat("Assuming SNV info has genome_id column ...\n")
     }
 
     qqcat("Genome ID in SNV information:\n")

R/plotKEGGPathway.R

@@ -82,7 +82,7 @@ plotKEGGPathway <- function(stana, species, pathway_id,
           lfcs[["Sum"]] <- apply(ko_tbl, 1, sum)
         } else {
             qqcat("@{sp}: @{names(cl)[1]} / @{names(cl)[2]}\n")
-            lfc[[sp]] <- L2FC(ko_tbl, cl[[1]], cl[[2]])
+            lfcs[[sp]] <- L2FC(ko_tbl, cl[[1]], cl[[2]])
         }
     } else {
         for (sp in species) {