update

NAMESPACE

@@ -61,6 +61,7 @@ export(plotKEGGPathway)
 export(plotMAF)
 export(plotPCA)
 export(plotSNVInfo)
+export(plotSNVSummary)
 export(returnGenes)
 export(reverseAnnot)
 export(setAnnotation)

R/plotKEGGPathway.R

@@ -32,7 +32,7 @@ plotKEGGPathway <- function(stana, species, pathway_id,
                             only_ko=FALSE, summarize=FALSE, nudge_y=0,
                             point_mode=FALSE, sp_colors=NULL,
                             point_size=1){
-    sum_flag <- FALSE
+    sum_flag <- FALSE	
     if (is.null(sp_colors)) {
     	## Assign random colors
     	sp_colors <- scales::brewer_pal(palette="RdBu")(length(species)) |>
@@ -91,7 +91,7 @@ plotKEGGPathway <- function(stana, species, pathway_id,
                 lfcs[[sp]] <- apply(ko_tbl, 1, sum)
             } else {
                 qqcat("@{sp}: @{names(cl)[1]} / @{names(cl)[2]}\n")
-                lfcs[[sp]] <- lL2FC(ko_tbl, cl[[1]], cl[[2]])
+                lfcs[[sp]] <- L2FC(ko_tbl, cl[[1]], cl[[2]], method="mod.t")
             }
         }        
     }

R/utils.R

@@ -81,4 +81,24 @@ plotSNVInfo <- function(stana, sp) {
         xlab("major_allele/minor_allele")+
         cowplot::theme_cowplot()+
         ggtitle(title)
+}
+
+#' plotSNVSummary
+#' @param stana stana object
+#' @param sp species_id
+#' @param param parameter to plot
+#' @export 
+#' @return ggplot object
+plotSNVSummary <- function(stana, sp, param="mean_coverage") {
+    df <- stana@snpsSummary
+    if (dim(df)[1]==0) {stop("SNV summary not available")}
+    df <- df %>% dplyr::filter(species_id == sp)
+    if (length(stana@cl)!=0) {
+        df[["group"]] <- listToNV(stana@cl)[df$sample_name]
+        ggplot(df, aes(x=group, y=.data[[param]])) +
+            geom_boxplot() + cowplot::theme_cowplot()
+    } else {
+        ggplot(df, aes(y=.data[[param]])) +
+            geom_boxplot() + cowplot::theme_cowplot()
+    }
 }