muxscan for mock and - maybe - performance improvements

.Rproj.user/F43DE67C/pcs/files-pane.pper

@@ -5,5 +5,5 @@
             "ascending": true
         }
     ],
-    "path": "~/NanoR"
+    "path": "~/NanoR/R"
 }

.Rproj.user/F43DE67C/pcs/source-pane.pper

@@ -1,3 +1,3 @@
 {
-    "activeTab": -1
+    "activeTab": 0
 }

.Rproj.user/F43DE67C/pcs/windowlayoutstate.pper

@@ -1,14 +1,14 @@
 {
     "left": {
-        "splitterpos": 345,
-        "topwindowstate": "HIDE",
-        "panelheight": 835,
-        "windowheight": 873
+        "splitterpos": 302,
+        "topwindowstate": "NORMAL",
+        "panelheight": 732,
+        "windowheight": 770
     },
     "right": {
-        "splitterpos": 519,
+        "splitterpos": 454,
         "topwindowstate": "NORMAL",
-        "panelheight": 835,
-        "windowheight": 873
+        "panelheight": 732,
+        "windowheight": 770
     }
 }

.Rproj.user/F43DE67C/persistent-state

@@ -1,8 +1,8 @@
 build-last-errors="[]"
 build-last-errors-base-dir="~/NanoR/"
-build-last-outputs="[{\"type\":0,\"output\":\"==> devtools::document(roclets = c('rd', 'collate', 'namespace'))\\n\\n\"},{\"type\":2,\"output\":\"ℹ Updating NanoR documentation\\n\"},{\"type\":2,\"output\":\"ℹ Loading NanoR\\n\"},{\"type\":2,\"output\":\"Warning: package ‘plotly’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘ggplot2’ was built under R version 4.1.1\\nWarning: package ‘scales’ was built under R version 4.1.1\\nWarning: package ‘data.table’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘dplyr’ was built under R version 4.1.1\\nWarning: package ‘tidyr’ was built under R version 4.1.1\\n\"},{\"type\":1,\"output\":\"Writing '\\u001B]8;;ide:run:pkgload::dev_help('alfredstats')\\u0007alfredstats.Rd\\u001B]8;;\\u0007'\\n\"},{\"type\":2,\"output\":\"Warning: Skipping 'NAMESPACE'\\n✖ It already exists and was not generated by roxygen2.\\n\"},{\"type\":1,\"output\":\"Documentation completed\\n\\n\"},{\"type\":0,\"output\":\"==> R CMD INSTALL --preclean --no-multiarch --with-keep.source NanoR\\n\\n\"},{\"type\":1,\"output\":\"* installing to library ‘/Users/davide.bolognini/Library/R/arm64/4.1/library’\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"* installing *source* package ‘NanoR’ ...\\n\"},{\"type\":1,\"output\":\"** using staged installation\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** R\\n\"},{\"type\":1,\"output\":\"** data\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"*** moving datasets to lazyload DB\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** inst\\n\"},{\"type\":1,\"output\":\"** byte-compile and prepare package for lazy loading\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"Warning messages:\\n\"},{\"type\":1,\"output\":\"1: package ‘plotly’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"2: package ‘ggplot2’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"3: package ‘scales’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"4: package ‘data.table’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"5: package ‘dplyr’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"6: package ‘tidyr’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** help\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"*** installing help indices\\n\"},{\"type\":1,\"output\":\"** building package indices\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package can be loaded from temporary location\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":2,\"output\":\"Warning: package ‘plotly’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘ggplot2’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘scales’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘data.table’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘dplyr’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘tidyr’ was built under R version 4.1.1\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package can be loaded from final location\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":2,\"output\":\"Warning: package ‘plotly’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘ggplot2’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘scales’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘data.table’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘dplyr’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘tidyr’ was built under R version 4.1.1\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\"},{\"type\":1,\"output\":\"* DONE (NanoR)\\n\"},{\"type\":1,\"output\":\"\"}]"
+build-last-outputs="[{\"type\":0,\"output\":\"==> devtools::document(roclets = c('rd', 'collate', 'namespace'))\\n\\n\"},{\"type\":1,\"output\":\"\\u001B[36mℹ\\u001B[39m Updating \\u001B[34m\\u001B[34mNanoR\\u001B[34m\\u001B[39m documentation\\n\"},{\"type\":1,\"output\":\"\\u001B[36mℹ\\u001B[39m Loading \\u001B[34m\\u001B[34mNanoR\\u001B[34m\\u001B[39m\\n\"},{\"type\":2,\"output\":\"Warning: package ‘plotly’ was built under R version 4.1.1\\nWarning: package ‘ggplot2’ was built under R version 4.1.1\\nWarning: package ‘scales’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘data.table’ was built under R version 4.1.1\\nWarning: package ‘dplyr’ was built under R version 4.1.1\\nWarning: package ‘tidyr’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: \\u001B[1m\\u001B[22mSkipping \\u001B]8;;file:///Users/davide.bolognini/NanoR/NAMESPACE\\u0007\\u001B[34mNAMESPACE\\u001B[39m\\u001B]8;;\\u0007\\n\\u001B[31m✖\\u001B[39m It already exists and was not generated by roxygen2.\\n\"},{\"type\":1,\"output\":\"Documentation completed\\n\\n\"},{\"type\":0,\"output\":\"==> R CMD INSTALL --preclean --no-multiarch --with-keep.source NanoR\\n\\n\"},{\"type\":1,\"output\":\"* installing to library ‘/Users/davide.bolognini/Library/R/arm64/4.1/library’\\n\"},{\"type\":1,\"output\":\"* installing *source* package ‘NanoR’ ...\\n\"},{\"type\":1,\"output\":\"** using staged installation\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** R\\n\"},{\"type\":1,\"output\":\"** data\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"*** moving datasets to lazyload DB\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** inst\\n\"},{\"type\":1,\"output\":\"** byte-compile and prepare package for lazy loading\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"Warning messages:\\n\"},{\"type\":1,\"output\":\"1: package ‘plotly’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"2: package ‘ggplot2’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"3: package ‘scales’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"4: package ‘data.table’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"5: package ‘dplyr’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"6: package ‘tidyr’ was built under R version 4.1.1 \\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** help\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"*** installing help indices\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** building package indices\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package can be loaded from temporary location\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":2,\"output\":\"Warning: package ‘plotly’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘ggplot2’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘scales’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘data.table’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘dplyr’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘tidyr’ was built under R version 4.1.1\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package can be loaded from final location\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":2,\"output\":\"Warning: package ‘plotly’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘ggplot2’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘scales’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘data.table’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘dplyr’ was built under R version 4.1.1\\n\"},{\"type\":2,\"output\":\"Warning: package ‘tidyr’ was built under R version 4.1.1\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"** testing if installed package keeps a record of temporary installation path\\n\"},{\"type\":1,\"output\":\"\"},{\"type\":1,\"output\":\"* DONE (NanoR)\\n\"},{\"type\":1,\"output\":\"\"}]"
 compile_pdf_state="{\"tab_visible\":false,\"running\":false,\"target_file\":\"\",\"output\":\"\",\"errors\":[]}"
 files.monitored-path=""
 find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":false,\"ignoreCase\":false,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOn\":[],\"matchOff\":[],\"replaceMatchOn\":[],\"replaceMatchOff\":[]},\"running\":false,\"replace\":false,\"preview\":false,\"gitFlag\":false,\"replacePattern\":\"\"}"
-imageDirtyState="0"
-saveActionState="0"
+imageDirtyState="1"
+saveActionState="-1"

.Rproj.user/F43DE67C/sources/prop/INDEX

@@ -1 +1,2 @@
 ~%2FNanoR%2FDESCRIPTION="300FBE73"
+~%2FNanoR%2FR%2Fmuxscan.R="68F33D03"

R/heatmap.R

@@ -113,23 +113,23 @@ heatmap<-function(summary,time=1,platform="minion",out) {
 
 	channels_activity_overtime<-channels_activity_overtime_pass<-matrix(0,ncol=n_channels, nrow=length(bins)-1)
 	channels_activity<-channels_activity_pass<-rep(0,n_channels)
-
+	
 	for (i in c(1:n_channels)) {
-
-		subtab<-subset(tab, (tab$channel == i))
+		
+		subtab<-tab[channel==i]
 		channels_activity[i]<-sum(subtab$sequence_length_template)
-		channels_activity_pass[i]<-sum(subset(subtab, (subtab$passes_filtering == TRUE))$sequence_length_template)
-
+		channels_activity_pass[i]<-sum(subtab[passes_filtering == TRUE]$sequence_length_template)
+		
 		for (l in c(1:(length(bins)-1))) {
-
-			from<-bins[l]
-			to<-bins[l+1]
-			subsubtab<-subset(subtab, (subtab$template_unix > from & subtab$template_unix <= to))
-			channels_activity_overtime[l,i]<-sum(subsubtab$sequence_length_template)
-			channels_activity_overtime_pass[l,i]<-sum(subset(subsubtab, (subsubtab$passes_filtering == TRUE))$sequence_length_template)
-			
+		
+		from<-bins[l]
+		to<-bins[l+1]
+		subsubtab<-subtab[template_unix > from & template_unix <= to]
+		channels_activity_overtime[l,i]<-sum(subsubtab$sequence_length_template)
+		channels_activity_overtime_pass[l,i]<-sum(subsubtab[passes_filtering == TRUE]$sequence_length_template)
+
 		}
-
+		
 	}
 
 	channels_activity_labels<-matrix("0",nrow=max(layout$row),ncol=max(layout$col))

R/muxscan.R

@@ -1,5 +1,5 @@
 #' @title muxscan
-#' @description generate an interactive HTML report with muxes status over time 
+#' @description generate an interactive HTML report with muxes status over time
 #' @param muxdata path to a mux scan data file from a single ONT run
 #' @param out path to HTML report
 #' @return HTML file
@@ -24,11 +24,22 @@ muxscan<-function(muxdata,out) {
 	csv<-as.data.frame(csv %>% group_by(B) %>% count(B, A))
 	csv<-as.data.frame(complete(csv,B,A))
 	csv[is.na(csv)] <- 0
-	csv<-unstack(form=n ~ A, x=csv)
+
+	if (length(unique(csv$B)) == 1) {
+
+	  fakedt<-csv
+	  fakedt$B<-2
+	  csv<-rbind(csv,fakedt)
+	  csv<-unstack(form=n ~ A, x=csv)[1,]
+
+	} else {
+
+	  csv<-unstack(form=n ~ A, x=csv)
+	}
+
 	csv<-setDT(csv, keep.rownames = TRUE)[]
 	csv$rn<-factor(csv$rn, levels=as.character(csv$rn))
 
-
 	f <- list(
 		size = 10,
 		color = "#7f7f7f"
@@ -38,7 +49,13 @@ muxscan<-function(muxdata,out) {
 
 	fig <- plot_ly(csv, x = ~rn, y = ~single_pore, type = "bar", name = "single_pore")
 	fig <- fig %>% add_trace(y = ~saturated, name = "saturated")
-	fig <- fig %>% add_trace(y = ~multiple, name = "multiple")
+
+	if ("multiple" %in% colnames(csv)) {
+
+	  fig <- fig %>% add_trace(y = ~multiple, name = "multiple")
+
+	}
+
 	fig <- fig %>% add_trace(y = ~other, name = "other")
 	fig <- fig %>% add_trace(y = ~zero, name = "zero")
 	fig <- fig %>% add_trace(y = ~unavailable, name = "unavailable")
@@ -54,4 +71,4 @@ muxscan<-function(muxdata,out) {
 	message("[",Sys.time(),"]"," done")
 
 
-}
+}