1. shinyMethyl
  2. R
  3. plotControlProbes.R
Browse code

Refactored package.

fortinj2 authored on 27/11/2022 18:46:13
Showing 1 changed files
R/plotControlProbes.R
History View file @ 9caf671
... ... 
@@ -1,31 +1,57 @@
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 ### To plot the internal controls
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-plotInternalControls <- function(y, col, main, sampleNames, bty="o"){
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+#' @importFrom graphics abline grid
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+plotInternalControls <- function(y,
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+                                 col,
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+                                 main,
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+                                 sampleNames,
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+                                 bty="o"
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+){
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     n <- length(y)
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     slideNames <- substr(sampleNames, 1, 10)
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-    plot(1:n, y, pch=20, cex=0.7, main = main, xlab = "Sample",
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-         ylab = "Control intensity", ylim = c(0, 1.3*max(y)),
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-         col = col, bty = bty)
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+    plot(seq_len(n),
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+         y,
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+         pch=20,
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+         cex=0.7,
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+         main=main,
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+         xlab="Sample",
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+         ylab="Control intensity",
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+         ylim=c(0, 1.3*max(y)),
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+         col=col,
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+         bty=bty)
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     grid()
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     abline(h=0, lty=3)
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 }
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 ### To add the selected array to the internal controls plot
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-addHoverPoints <- function(y, sampleNames, selectedSamples=c()){
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+#' @importFrom graphics points
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+addHoverPoints <- function(y,
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+                           sampleNames,
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+                           selectedSamples=c()
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+){
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     ## To put a circle around the last entry:
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     n <- length(selectedSamples)
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     if (n>=1){
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-        points(selectedSamples[n], y[selectedSamples[n]], pch = 1,
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-               cex = 3, lwd = 3)
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-        points(selectedSamples[1:n], y[selectedSamples[1:n]],
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-               pch = 17, cex = 1, lwd = 3)
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+        points(selectedSamples[n],
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+               y[selectedSamples[n]],
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+               pch = 1,
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+               cex = 3,
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+               lwd = 3)
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+        points(selectedSamples[seq_len(n)],
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+               y[selectedSamples[seq_len(n)]],
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+               pch = 17,
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+               cex = 1,
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+               lwd = 3)
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     }
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 }
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-returnControlStat <- function(controlType, greenControls,
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-                              redControls, controlNames){
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+returnControlStat <- function(controlType,
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+                              greenControls,
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+                              redControls,
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+                              controlNames
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+){
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     index <- match(controlType, controlNames)
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     greenControls.current <- greenControls[[index]]
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-    redControls.current <- redControls[[index]]
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+    redControls.current   <- redControls[[index]]
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     if (controlType=="BISULFITE CONVERSION I"){
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         controlStat <- (apply(greenControls.current[1:3,], 2, mean) +
Browse code

Adds oposSOM/ pepStat/ Polyfit/ pRolocGUI/ Pviz/ shinyMethyl/ to the repos.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl@92064 bc3139a8-67e5-0310-9ffc-ced21a209358

m.carlson authored on 01/07/2014 20:38:11
Showing 1 changed files
R/plotControlProbes.R
History View file @ 4978515
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,54 @@
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+### To plot the internal controls
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+plotInternalControls <- function(y, col, main, sampleNames, bty="o"){
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+    n <- length(y)
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+    slideNames <- substr(sampleNames, 1, 10)
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+    plot(1:n, y, pch=20, cex=0.7, main = main, xlab = "Sample",
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+         ylab = "Control intensity", ylim = c(0, 1.3*max(y)),
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+         col = col, bty = bty)
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+    grid()
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+    abline(h=0, lty=3)
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+}
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+
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+### To add the selected array to the internal controls plot
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+addHoverPoints <- function(y, sampleNames, selectedSamples=c()){
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+    ## To put a circle around the last entry:
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+    n <- length(selectedSamples)
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+    if (n>=1){
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+        points(selectedSamples[n], y[selectedSamples[n]], pch = 1,
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+               cex = 3, lwd = 3)
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+        points(selectedSamples[1:n], y[selectedSamples[1:n]],
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+               pch = 17, cex = 1, lwd = 3)
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+    }
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+}
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+
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+returnControlStat <- function(controlType, greenControls,
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+                              redControls, controlNames){
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+    index <- match(controlType, controlNames)
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+    greenControls.current <- greenControls[[index]]
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+    redControls.current <- redControls[[index]]
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+
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+    if (controlType=="BISULFITE CONVERSION I"){
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+        controlStat <- (apply(greenControls.current[1:3,], 2, mean) +
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+                        apply(redControls.current[7:9,], 2, mean))/2
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+    } else {
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+        if (controlType=="BISULFITE CONVERSION II"){
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+            controlStat <- apply(redControls.current, 2, mean)
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+        } else {
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+            if (controlType=="EXTENSION"){
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+                controlStat <- (apply(greenControls.current[3:4,], 2, mean) +
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+                                apply(redControls.current[1:2,], 2, mean))/2
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+            } else {
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+                if (controlType=="NEGATIVE"){
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+                    controlStat <- (apply(greenControls.current, 2, mean) +
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+                                    apply(redControls.current, 2, mean))/2
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+                } else {
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+                    if (controlType=="HYBRIDIZATION"){
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+                        controlStat <- apply(greenControls.current, 2, mean)
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+                    } else {controlStat <- apply(greenControls.current, 2, mean)
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+                        }
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+                }
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+            }
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+        }
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+    }
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+    return(controlStat)
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+}