Update digestR.R

Author: DDesmonts

R/digestR.R

@@ -1327,102 +1327,102 @@ popupGui <- function(dev){
 }
 
 # Displays the digestR splash screen
-# splashScreen <- function(){
+splashScreen <- function(){
 
-#   par(mar=defaultSettings$mar, cex.axis=defaultSettings$cex.axis, 
-#       cex.main=defaultSettings$cex.main, bg='black')
-#   colMain <- '#b4d0f3'
-#   colBack <- '#0065ca'
-#   plot(0, 0, type='n', xlab='', ylab='', col.axis='black')
-#   # Define your color palette
-#   #colMain <- '#FF5733'  # A warm main color
-#   #colBack <- '#2E86C1'  # A contrasting background color
+  par(mar=defaultSettings$mar, cex.axis=defaultSettings$cex.axis, 
+      cex.main=defaultSettings$cex.main, bg='black')
+  colMain <- '#b4d0f3'
+  colBack <- '#0065ca'
+  plot(0, 0, type='n', xlab='', ylab='', col.axis='black')
+  # Define your color palette
+  #colMain <- '#FF5733'  # A warm main color
+  #colBack <- '#2E86C1'  # A contrasting background color
 
-#   # Letter positions and colors
-#   letters <- c('D', 'I', 'G', 'E', 'S', 'T', 'R')
-#   colors <- c(colMain, colMain, colMain, colMain, colMain, colMain, colBack)
-#   cex_values <- c(7, 7, 7, 7, 7, 7, 6.5)
-#   offset_values <- c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.4)
+  # Letter positions and colors
+  letters <- c('D', 'I', 'G', 'E', 'S', 'T', 'R')
+  colors <- c(colMain, colMain, colMain, colMain, colMain, colMain, colBack)
+  cex_values <- c(7, 7, 7, 7, 7, 7, 6.5)
+  offset_values <- c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.4)
 
-#   # Loop to create and position letters
-#   for (i in 1:length(letters)) {
-#     text(-0.75 + (i-1)*0.25, 0.2, letters[i], col=colors[i], cex=cex_values[i], pos=3, offset=offset_values[i])
-#   }
+  # Loop to create and position letters
+  for (i in 1:length(letters)) {
+    text(-0.75 + (i-1)*0.25, 0.2, letters[i], col=colors[i], cex=cex_values[i], pos=3, offset=offset_values[i])
+  }
 
-#   # Add a decorative 'R' in a different color
-#   text(0.70, 0.2, 'R', col='#E74C3C', cex=5.5, pos=3, offset=0.4)
+  # Add a decorative 'R' in a different color
+  text(0.70, 0.2, 'R', col='#E74C3C', cex=5.5, pos=3, offset=0.4)
 
-#   # Other text elements (modify as needed)
-#   text(0, 0.08, 'Digestomics Analyzer', col=colMain, cex=2.5, font=1)
-#   text(0, -0.15, paste('version 1.0.0', pkgVar$version), col=colMain, font=3)
-#   text(0, -0.25, 'gp() - Generate New Proteome', col=colMain)
-#   text(0, -0.35, 'pm() - Process Mascot files', col=colMain)
-#   text(0, -0.45, 'fo() - Open *.dcf files', col=colMain)
+  # Other text elements (modify as needed)
+  text(0, 0.08, 'Digestomics Analyzer', col=colMain, cex=2.5, font=1)
+  text(0, -0.15, paste('version 1.0.0', pkgVar$version), col=colMain, font=3)
+  text(0, -0.25, 'gp() - Generate New Proteome', col=colMain)
+  text(0, -0.35, 'pm() - Process Mascot files', col=colMain)
+  text(0, -0.45, 'fo() - Open *.dcf files', col=colMain)
 
-#   # Force the graphics device to refresh
-#   dev.flush()
-# }
+  # Force the graphics device to refresh
+  dev.flush()
+}
 
-# Displays the digestR splash screen
-splashScreen <- function(){
+# # Displays the digestR splash screen
+# splashScreen <- function(){
 
-library(png)
-  par(mar=defaultSettings$mar, cex.axis=defaultSettings$cex.axis, 
-      cex.main=defaultSettings$cex.main, bg='black')
-  colMain <- '#b4d0f3'
-  colBack <- '#0065ca'
-  plot(0, 0, type='n', xlab='', ylab='', col.axis='black')
+# library(png)
+#   par(mar=defaultSettings$mar, cex.axis=defaultSettings$cex.axis, 
+#       cex.main=defaultSettings$cex.main, bg='black')
+#   colMain <- '#b4d0f3'
+#   colBack <- '#0065ca'
+#   plot(0, 0, type='n', xlab='', ylab='', col.axis='black')
 
- # Load the image and get its dimensions
-  img_path <- system.file("extdata", "DigestRpicture.png", package = "digestR")
-  img <- readPNG(img_path)  
+#  # Load the image and get its dimensions
+#   img_path <- system.file("extdata", "DigestRpicture.png", package = "digestR")
+#   img <- readPNG(img_path)  
 
-  xlim <- c(-1.5, 1.5)  # Adjust the x-axis limits as needed
-  ylim <- c(-1.5, 1.5)  # Adjust the y-axis limits as needed
+#   xlim <- c(-1.5, 1.5)  # Adjust the x-axis limits as needed
+#   ylim <- c(-1.5, 1.5)  # Adjust the y-axis limits as needed
 
-  # Create plot with no margins and appropriate limits
-  par(mar=c(0,0,0,0), bg='#0d0d0d')
-  plot(0, 0, type='n', xlab='', ylab='', axes=FALSE, xlim=xlim, ylim=ylim)
+#   # Create plot with no margins and appropriate limits
+#   par(mar=c(0,0,0,0), bg='#0d0d0d')
+#   plot(0, 0, type='n', xlab='', ylab='', axes=FALSE, xlim=xlim, ylim=ylim)
 
-  # Display the image, stretched to fit the plot region
-  rasterImage(img, xlim[1], ylim[1], xlim[2], ylim[2])
+#   # Display the image, stretched to fit the plot region
+#   rasterImage(img, xlim[1], ylim[1], xlim[2], ylim[2])
 
-  # Letter positions and modern color scheme for "PANDAS"
-  letters <- c('P', 'A', 'N', 'D', 'A', 'S')
-  x_positions <- c(-0.9, -0.6, -0.3, 0.0, 0.3, 0.6)  # Custom X positions for each letter
-  y_positions <- c(0.62, 0.62, 0.62, 0.62, 0.62, 0.62)  # Use different y positions as needed
-  colors <- rep('#4da6ff', 6)  #
-  cex_values <- rep(5, 6)  # Reduced font size for smaller splash screen
+#   # Letter positions and modern color scheme for "PANDAS"
+#   letters <- c('P', 'A', 'N', 'D', 'A', 'S')
+#   x_positions <- c(-0.9, -0.6, -0.3, 0.0, 0.3, 0.6)  # Custom X positions for each letter
+#   y_positions <- c(0.62, 0.62, 0.62, 0.62, 0.62, 0.62)  # Use different y positions as needed
+#   colors <- rep('#4da6ff', 6)  #
+#   cex_values <- rep(5, 6)  # Reduced font size for smaller splash screen
 
-  # Add shadow effect to the letters for depth
-  shadow_col <- '#00000050'  # Semi-transparent black shadow
-  for (i in 1:length(letters)) {
-    text(x_positions[i] + 0.02, y_positions[i] - 0.02, letters[i], col=shadow_col, cex=cex_values[i], pos=3)
-    text(x_positions[i], y_positions[i], letters[i], col=colors[i], cex=cex_values[i], pos=3)
-  }
+#   # Add shadow effect to the letters for depth
+#   shadow_col <- '#00000050'  # Semi-transparent black shadow
+#   for (i in 1:length(letters)) {
+#     text(x_positions[i] + 0.02, y_positions[i] - 0.02, letters[i], col=shadow_col, cex=cex_values[i], pos=3)
+#     text(x_positions[i], y_positions[i], letters[i], col=colors[i], cex=cex_values[i], pos=3)
+#   }
 
-  # Add black shadow for the title "Peptide Analyzer of Naturally Digested Amino acid Sequences"
-  # Shadow for "Peptide Analyzer of"
-  text(0, -0.4, 'Peptide Analyzer of', col='black', cex=1.80, font=2.3)  # Black shadow
-  # Main text for "Peptide Analyzer of"
-  text(0, -0.4, 'Peptide Analyzer of', col='#4da6ff', cex=1.8, font=2)  # Main text
+#   # Add black shadow for the title "Peptide Analyzer of Naturally Digested Amino acid Sequences"
+#   # Shadow for "Peptide Analyzer of"
+#   text(0, -0.4, 'Peptide Analyzer of', col='black', cex=1.80, font=2.3)  # Black shadow
+#   # Main text for "Peptide Analyzer of"
+#   text(0, -0.4, 'Peptide Analyzer of', col='#4da6ff', cex=1.8, font=2)  # Main text
 
-  # Shadow for "Naturally Digested Amino acid sequences"
-  text(0, -0.53, 'Naturally Digested Amino acid Sequences', col='black', cex=1.80, font=2.3)  # Black shadow
-  # Main text for "Naturally Digested Amino acid sequences"
-  text(0, -0.53, 'Naturally Digested Amino acid Sequences', col='#4da6ff', cex=1.8, font=2)  # Main text
+#   # Shadow for "Naturally Digested Amino acid sequences"
+#   text(0, -0.53, 'Naturally Digested Amino acid Sequences', col='black', cex=1.80, font=2.3)  # Black shadow
+#   # Main text for "Naturally Digested Amino acid sequences"
+#   text(0, -0.53, 'Naturally Digested Amino acid Sequences', col='#4da6ff', cex=1.8, font=2)  # Main text
 
-  # Version and command text, shifted further downwards
-  text(0, -0.75, paste('version 1.0.0', pkgVar$version), col='#00b3b3', font=2)  # Dynamic color
+#   # Version and command text, shifted further downwards
+#   text(0, -0.75, paste('version 1.0.0', pkgVar$version), col='#00b3b3', font=2)  # Dynamic color
 
-  # Clean, minimal function list with better spacing and shifted downwards
-  text(0, -0.86, 'gp() - Generate New Proteome', col='#00b3b3', cex=1.1, font = 2)  # Light blue
-  text(0, -0.94, 'pm() - Process Mascot files', col='#00b3b3', cex=1.1, font = 2)  # Light blue
-  text(0, -1.02, 'fo() - Open *.dcf files', col='#00b3b3', cex=1.1, font = 2)  # Light blue
+#   # Clean, minimal function list with better spacing and shifted downwards
+#   text(0, -0.86, 'gp() - Generate New Proteome', col='#00b3b3', cex=1.1, font = 2)  # Light blue
+#   text(0, -0.94, 'pm() - Process Mascot files', col='#00b3b3', cex=1.1, font = 2)  # Light blue
+#   text(0, -1.02, 'fo() - Open *.dcf files', col='#00b3b3', cex=1.1, font = 2)  # Light blue
 
-  # Force the graphics device to refresh
-  dev.flush()
-}
+#   # Force the graphics device to refresh
+#   dev.flush()
+# }
 
 ##################################################################################