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Static_Bubble_Plot_Cmdln.R |
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| diff -r aa0debcd27be -r efc13028725c Static_Bubble_Plot_Cmdln.R --- a/Static_Bubble_Plot_Cmdln.R Wed May 11 11:14:45 2016 -0400 +++ b/Static_Bubble_Plot_Cmdln.R Wed May 11 11:15:31 2016 -0400 |
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| b'@@ -3,47 +3,47 @@\n # Author: Brent Kuenzi\n ################################## Dependencies ###################################################\n library(dplyr); library(tidyr); library(ggplot2); library(ggrepel)\n-colors <- c("Air Force blue" = "#5D8AA8", "Alice blue" = "#F0F8FF", "Alizarin crimson" = "#E32636", "Almond" = "#EFDECD", "Amaranth" = "#E52B50", "Amber" = "#FFBF00", "American rose" = "#FF033E", "Amethyst" = "#9966CC", "Android Green" = "#A4C639", "Anti flash white" = "#F2F3F4", "Antique brass" = "#CD9575", "Antique fuchsia" = "#915C83", "Antique white" = "#FAEBD7", "Ao" = "#008000", "Apple green" = "#8DB600", "Apricot" = "#FBCEB1", "Aqua" = "#00FFFF", "Aquamarine" = "#7FFFD4", "Army green" = "#4B5320", "Arsenic" = "#3B444B", "Arylide yellow" = "#E9D66B", "Ash gray" = "#B2BEB5", "Asparagus" = "#87A96B", "Atomic tangerine" = "#FF9966", "Auburn" = "#A52A2A", "Aureolin" = "#FDEE00", "AuroMetalSaurus" = "#6E7F80", "Awesome" = "#FF2052", "Azure" = "#007FFF", "Azure mist" = "#F0FFFF", "Baby blue" = "#89CFF0", "Baby blue eyes" = "#A1CAF1", "Baby pink" = "#F4C2C2", "Ball Blue" = "#21ABCD", "Banana Mania" = "#FAE7B5", "Banana yellow" = "#FFE135", "Battleship gray" = "#848482", "Bazaar" = "#98777B", "Beau blue" = "#BCD4E6", "Beaver" = "#9F8170", "Beige" = "#F5F5DC", "Bisque" = "#FFE4C4", "Bistre" = "#3D2B1F", "Bittersweet" = "#FE6F5E", "Obsidian" = "#000000", "Onyx" = "#000000", "Lost Soul" = "#000000", "Midnight" = "#000000", "Rolling Blackout" = "#000000", "Sleeping Panther" = "#000000", "Void by Armani" = "#000000", "Blanched Almond" = "#FFEBCD", "Bleu de France" = "#318CE7", "Blizzard Blue" = "#ACE5EE", "Blond" = "#FAF0BE", "Blue" = "#0000FF", "Blue Bell" = "#A2A2D0", "Blue Gray" = "#6699CC", "Blue green" = "#00DDDD", "Blue violet" = "#8A2BE2", "Blush" = "#DE5D83", "Bole" = "#79443B", "Bondi blue" = "#0095B6", "Boston University Red" = "#CC0000", "Brandeis blue" = "#0070FF", "Brass" = "#B5A642", "Brick red" = "#CB4154", "Bright cerulean" = "#1DACD6", "Bright green" = "#66FF00", "Bright lavender" = "#BF94E4", "Bright maroon" = "#C32148", "Bright pink" = "#FF007F", "Bright turquoise" = "#08E8DE", "Bright ube" = "#D19FE8", "Brilliant lavender" = "#F4BBFF", "Brilliant rose" = "#FF55A3", "Brink pink" = "#FB607F", "British racing green" = "#004225", "Bronze" = "#CD7F32", "Brown" = "#964B00", "Bubble gum" = "#FFC1CC", "Bubbles" = "#E7FEFF", "Buff" = "#F0DC82", "Bulgarian rose" = "#480607", "Burgundy" = "#800020", "Burlywood" = "#DEB887", "Burnt orange" = "#CC5500", "Burnt sienna" = "#E97451", "Burnt umber" = "#8A3324", "Byzantine" = "#BD33A4", "Byzantium" = "#702963", "Cadet" = "#536872", "Cadet blue" = "#5F9EA0", "Cadet gray" = "#91A3B0", "Cadmium Green" = "#006B3C", "Cadmium Orange" = "#ED872D", "Cadmium Red" = "#E30022", "Cadmium Yellow" = "#FFF600", "Cal Poly Pomona green" = "#1E4D2B", "Cambridge Blue" = "#A3C1AD", "Camel" = "#C19A6B", "Camouflage green" = "#78866B", "Canary yellow" = "#FFEF00", "Candy apple red" = "#FF0800", "Candy pink" = "#E4717A", "Capri" = "#00BFFF", "Caput mortuum" = "#592720", "Cardinal" = "#C41E3A", "Caribbean green" = "#00CC99", "Carmine" = "#960018", "Carmine pink" = "#EB4C42", "Carmine red" = "#FF0038", "Carnation pink" = "#FFA6C9", "Carnelian" = "#B31B1B", "Carolina blue" = "#99BADD", "Carrot orange" = "#ED9121", "Ceil" = "#92A1CF", "Celadon" = "#ACE1AF", "Celestial blue" = "#4997D0", "Cerise" = "#DE3163", "Cerise pink" = "#EC3B83", "Cerulean" = "#007BA7", "Cerulean blue" = "#2A52BE", "CG Blue" = "#007AA5", "CG Red" = "#E03C31", "Chamoisee" = "#A0785A", "Champagne" = "#F7E7CE", "Charcoal" = "#36454F", "Chartreuse" = "#DFFF00", "Cherry blossom pink" = "#FFB7C5", "Chestnut" = "#CD5C5C", "Chocolate" = "#7B3F00", "Chrome yellow" = "#FFA700", "Cinereous" = "#98817B", "Cinnabar" = "#E34234", "Cinnamon" = "#D2691E", "Citrine" = "#E4D00A", "Classic rose" = "#FBCCE7", "Cobalt" = "#0047AB", "Coffee" = "#C86428", "Columbia blue" = "#9BDDFF", "Cool black" = "#002E63", "Cool gray" = "#8C92AC", "Copper" = "#B87'..b'affre"="#0014A8","Zinnwalditebrown"="#2C1608")\n ################################# Read in Data ####################################################\n ## REQUIRED INPUTS ##\n # 1) listfile (filename)\n-listfile <- "EGFR_list.txt"\n+#listfile <- "EGFR_list.txt"\n # 2) Prey File (filename)\n-preyfile <- "EGFR_prey.txt"\n+#preyfile <- "EGFR_prey.txt"\n # 3) crapome File (filename or FALSE)\n-crapfile <- "EGFR_crap.txt"\n+#crapfile <- "EGFR_crap.txt"\n # 4) Inter File (filename)\n-interfile <- "inter.txt"\n+#interfile <- "inter.txt"\n # 5) X axis ("ln(NSAF)","SpecSum", "log2(FoldChange)", "SaintScore", "logOddsScore","NSAFScore")\n-input.main.x <- "ln(NSAF)"\n+#input.main.x <- "ln(NSAF)"\n # 6) Y axis ("ln(NSAF)","SpecSum", "log2(FoldChange)", "SaintScore", "logOddsScore","NSAFScore")\n-input.main.y <- "log2(FoldChange)"\n+#input.main.y <- "log2(FoldChange)"\n # 7) Bubble Size ("ln(NSAF)","SpecSum", "log2(FoldChange)", "SaintScore", "logOddsScore","NSAFScore")\n-input.main.size <- "SpecSum"\n+#input.main.size <- "SpecSum"\n # 8) Coloring ("fixed" or "crapome")\n-input.main.color <- "crapome"\n+#input.main.color <- "crapome"\n # 9) Saint Score Cutoff (0 - 1)\n-input.SS_cutoff <- 0.8\n+#input.SS_cutoff <- 0.8\n # 10) Fold change Cutoff (-inf - inf)\n-input.FC_cutoff <- 0\n+#input.FC_cutoff <- 0\n # 11) NSAF Score Cutoff (-inf - inf)\n-input.NS_cutoff <- 0\n+#input.NS_cutoff <- 0\n # 12) Plotting Theme ("Default","b/w","minimal","classic","dark","linedraw")\n-input.plot_theme <- "Default"\n+#input.plot_theme <- "Default"\n # 13) Bubble Labels ("none",">cutoff","all")\n-input.bubble_label <- ">cutoff"\n+#input.bubble_label <- ">cutoff"\n # 14) Label Color ("white","black")\n-input.label_color <- "black"\n+#input.label_color <- "black"\n # 15) Bubble Color (colors listed above)\n-input.bubble_color <- colors[["Alizarin crimson"]]\n+#input.bubble_color <- colors[["Alizarin crimson"]]\n # 16) Bubble outline color ("white","black")\n-input.outline_color <- "black"\n+#input.outline_color <- "black"\n # 17) CRAPome Filtered Bubble Color (colors listed above)\n-input.filt_color <- colors[["Tan"]]\n+#input.filt_color <- colors[["Tan"]]\n # 18) Bubble scale ((0-100),(0-100)) # SECOND NUMBER MUST BE LARGER THAN OR EQUAL TO THE FIRST\n-input.plot_scale <- c(0,10)\n+#input.plot_scale <- c(0,10)\n # 19) File Type (".pdf",".png",".tif",".svg",".eps",".jpg")\n-input.file_type <- ".png"\n+#input.file_type <- ".png"\n \n ################################################################################\n # Define merge function and calculate crapome %\n@@ -181,13 +181,23 @@\n main.data$control_NSAF <- NULL; main.data$temp <- NULL\n main.data$ctrl_mean <- NULL\n ################################################################################\n+if (args[7] == "fixed"){\n+\tinput.main.size <- "SpecSum"\n+\tinput.plot_scale <- c(2,2)\n+} else {\n+\tinput.main.size <- args[7]\n+\tinput.plot_scale <- c(0,10)\n+}\n+input.bubble_color <- colors[[args[15]]]\n+input.filt_color <- colors[[args[17]]]\n bubblebeam(main.data = main.data, main.exclude = FALSE,main.x = args[5],\n- main.y = args[6],main.size = args[7],main.color = colors[[args[8]]],\n- SS_cutoff = args[8],FC_cutoff = args[9],\n- NS_cutoff = args[10], plot_theme = args[11],\n- bubble_label = args[12],label_color = args[13],\n- bubble_color = colors[[args[14]]], outline_color = args[15],\n- filt_color = colors[[args[16]]], plot_scale = c(0,10), \n+ main.y = args[6],main.size = input.main.size,main.color = args[8],\n+ SS_cutoff = args[9],FC_cutoff = args[10],\n+ NS_cutoff = args[11], plot_theme = args[12],\n+ bubble_label = args[13],label_color = args[14],\n+ bubble_color = input.bubble_color, outline_color = args[16],\n+ filt_color = input.filt_color, plot_scale = input.plot_scale, \n file_type = ".png")\n ################################################################################\n \n+\n' |