polishing

jlmaier12 · Dec 12, 2024 · 6ff8f10 · 6ff8f10
1 parent b904dad
commit 6ff8f10
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Showing 4 changed files with 12 additions and 8 deletions.
diff --git a/R/TrIdentClassifier.R b/R/TrIdentClassifier.R
@@ -144,7 +144,7 @@ TrIdentClassifier <- function(VLPpileup,
         " of the prophage-like classifications are mixed, i.e. heterogenously
         integrated into their bacterial host population"
     )
-    print(plot(resultsHisto(summaryList, suggFiltThresh)))
+    plot(resultsHisto(summaryList, suggFiltThresh))
     if (missing(SaveFilesTo) == FALSE) {
         ifelse(!dir.exists(paths = paste0(SaveFilesTo, "\\TrIdentOutput")),
             dir.create(paste0(SaveFilesTo, "\\TrIdentOutput")),

diff --git a/R/plotTrIdentResults.R b/R/plotTrIdentResults.R
@@ -105,7 +105,7 @@ plotTrIdentResults <- function(VLPpileup,
                 axis.line = element_line(colour = "black"),
                 text = element_text(size = 14),
                 axis.text = element_text(size = 10),
-                plot.subtitle = element_text(size = 10),
+                plot.subtitle = element_text(size = 11),
                 plot.margin = margin(
                     t = 0,
                     r = 6,

diff --git a/R/specTransductionPlot.R b/R/specTransductionPlot.R
@@ -34,12 +34,12 @@ specTransductionPlot <-
         position <- logcoverage <- NULL
         if (classifSumm[
             which(classifSumm[, 1] == contigName),
-            6
+            8
         ] == "Elevated") {
             prophageLikeInfo <- "Highly active/abundant prophage-like element"
         } else if (classifSumm[
             which(classifSumm[, 1] == contigName),
-            6
+            8
         ] == "Depressed") {
             prophageLikeInfo <-
                 "Not homogenously present/integrated prophage-like element"
@@ -82,15 +82,15 @@ specTransductionPlot <-
                 theme(
                     panel.grid.major = element_blank(),
                     panel.grid.minor = element_blank(),
-                    plot.subtitle = element_text(size = 10),
+                    plot.subtitle = element_text(size = 11),
                     panel.background = element_blank(),
                     axis.line = element_line(colour = "black"),
-                    text = element_text(size = 15)
+                    text = element_text(size = 15),
+                    plot.title = element_text(size = 12)
                 ) +
                 labs(
                     title = paste(
-                        contigName, classifPatternMatches[[i]][[8]],
-                        prophageLikeInfo
+                        contigName, prophageLikeInfo
                     ),
                     subtitle = paste(
                         "Specialized transduction on left:",

diff --git a/R/specializedTransductionID.R b/R/specializedTransductionID.R
@@ -130,6 +130,10 @@ specializedTransductionID <- function(VLPpileup,
         specTransCount,
         " contigs have potential specialized transduction"
     )
+    if (logScale == FALSE) message(
+      "We recommend that you also view the results of this search with
+      logScale=TRUE"
+      )
     names(plots) <- specTransSumm[, 1]
     specTransList <- list(summaryTable = specTransSumm, Plots = plots)
     if (missing(SaveFilesTo) == FALSE) {