First minor updates 2021
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hyginn
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# Purpose: Reference to graphical output in R.
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#
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#
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# Version: 2.0
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# Version: 2.1
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#
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# Date: 2017 09 - 2020 10
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# Date: 2017 09 - 2021 09
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# V 2.1 First minor updates 2021
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# V 2.0 Comprehensive reference with basic and advanced options based on
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# an integrated yeast gene expression dataset. Full rewrite of most
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# sections.
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# V 1.1 Stylistic improvements, code polish, and additional examples
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# V 1.0 Digest from "plotting reference" files
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#
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# ToDo:
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# ToDo: Demo 6.3.2 in parallel plots
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#
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#
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> ------------------------------------------------------------------
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#TOC> 01 INITIALIZE 67
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#TOC> 02 THIS REFERENCE ... 72
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#TOC> 02.1 Dataset Documentation 79
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#TOC> 03 PROPORTIONS AND DISTRIBUTIONS 191
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#TOC> 03.1 barplot() 196
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#TOC> 03.2 pie() 220
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#TOC> 03.3 boxplot() 252
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#TOC> 03.4 hist() 310
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#TOC> 03.4.1 overlaying histograms 355
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#TOC> 04 THE plot() FUNCTION 398
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#TOC> 04.1 line plots 402
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#TOC> 05 ENCODING INFORMATION: SYMBOL, SIZE, COLOR 501
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#TOC> 05.1 pch ("plotting character" symbols) 507
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#TOC> 05.1.1 Line types 682
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#TOC> 06 COLOUR 704
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#TOC> 06.1 Colours by number 712
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#TOC> 06.2 Colours by name 730
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#TOC> 06.3 Colours as hex-triplets 756
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#TOC> 06.3.1 Inbuilt palettes 811
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#TOC> 06.3.2 Custom palettes 887
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#TOC> 06.3.3 Transparency: The Alpha Channel 937
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#TOC> 06.4 abline(), lines() and segments() 983
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#TOC> 07 AXES 1017
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#TOC> 08 LEGENDS 1054
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#TOC> 08.1 basic legends 1057
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#TOC> 08.2 Color bars 1061
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#TOC> 09 LAYOUT 1180
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#TOC> 10 TEXT 1215
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#TOC> 11 DRAWING ON PLOTS 1243
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#TOC> 12 IMAGES 1310
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#TOC> 13 CONTOUR LINES 1315
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#TOC> 14 3D PLOTS 1320
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#TOC> 15 GRAPHS AND NETWORKS 1325
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#TOC> 16 OTHER GRPAHICS PACKAGES 1330
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#TOC> 17 INTERACTIVE PLOTS 1354
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#TOC> 17.1 locator() 1358
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#TOC> 17.2 plotly:: 1361
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> -------------------------------------------------------------------
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#TOC> 01 INITIALIZE 69
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#TOC> 02 THIS REFERENCE ... 74
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#TOC> 02.1 Dataset Documentation 81
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#TOC> 03 PROPORTIONS AND DISTRIBUTIONS 193
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#TOC> 03.1 barplot() 198
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#TOC> 03.2 pie() 222
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#TOC> 03.3 boxplot() 254
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#TOC> 03.4 hist() 312
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#TOC> 03.4.1 overlaying histograms 357
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#TOC> 04 THE plot() FUNCTION 400
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#TOC> 04.1 line plots 404
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#TOC> 05 ENCODING INFORMATION: SYMBOL, SIZE, COLOuR 503
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#TOC> 05.1 pch ("plotting character" symbols) 509
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#TOC> 05.1.1 Line types 684
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#TOC> 05.2 cex ("character expansion" size) 708
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#TOC> 06 COLOUR 768
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#TOC> 06.1 Colours by number 776
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#TOC> 06.2 Colours by name 794
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#TOC> 06.3 Colours as hex-triplets 820
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#TOC> 06.3.1 Inbuilt palettes 875
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#TOC> 06.3.2 Custom palettes 952
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#TOC> 06.3.3 Transparency: The Alpha Channel 1002
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#TOC> 06.4 abline(), lines() and segments() 1047
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#TOC> 07 AXES 1081
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#TOC> 08 LEGENDS 1118
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#TOC> 08.1 basic legends 1121
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#TOC> 08.2 Color bars 1125
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#TOC> 09 LAYOUT 1246
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#TOC> 10 TEXT 1281
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#TOC> 11 DRAWING ON PLOTS 1309
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#TOC> 12 IMAGES 1376
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#TOC> 13 CONTOUR LINES 1381
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#TOC> 14 3D PLOTS 1386
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#TOC> 15 GRAPHS AND NETWORKS 1391
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#TOC> 16 OTHER GRPAHICS PACKAGES 1396
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#TOC> 17 INTERACTIVE PLOTS 1420
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#TOC> 17.1 locator() 1424
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#TOC> 17.2 plotly:: 1427
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#TOC>
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#TOC> ==========================================================================
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@@ -352,7 +354,7 @@ hist(SC$mdl$peaks, # gene expression first peaks
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col = myPal(81)) # get 81 color values from myPal()
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# === 03.4.1 overlaying histograms
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# === 03.4.1 overlaying histograms
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# Histograms can be plotted one-over another to compare them
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# Example: when do genes with different GO term annotations first peak?
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@@ -679,7 +681,7 @@ legend ("bottom",
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box.col = "#DDDDDD",
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bg = "#FFFFFF")
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# === 05.1.1 Line types
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# === 05.1.1 Line types
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# Basically all plots take arguments lty to define the line type, and lwd
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# to define line width
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@@ -703,7 +705,7 @@ for (i in 1:10) {
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# == 05.1 cex ("character expansion" size) =============================
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# == 05.2 cex ("character expansion" size) =================================
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# The size of characters can be controlled with the cex parameter. cex takes a
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# vector of numbers, mapped to the vecors of plotted elements. The usual R
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@@ -870,7 +872,7 @@ N <- 40
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barplot(rep(1, N), col = col2hex(myCols,pal=TRUE,N=N) )
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# === 06.3.1 Inbuilt palettes
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# === 06.3.1 Inbuilt palettes
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# In R, a palette is a function (!) that takes a number as its argument and
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# returns that number of colors, those colors can then be used to color points
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@@ -947,7 +949,7 @@ RColorBrewer::display.brewer.all(colorblindFriendly = TRUE)
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plotPal(RColorBrewer::brewer.pal(11, "PuOr"), N = 11)
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# === 06.3.2 Custom palettes
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# === 06.3.2 Custom palettes
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#
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# Bespoke palettes are easily created with colorRampPalette(). The function
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# returns a palette, i.e. a function (not a vector of colors). You assign the
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@@ -997,7 +999,7 @@ plotPal(myOutliers)
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# also an option to extract palettes from user-supplied images.
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# === 06.3.3 Transparency: The Alpha Channel
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# === 06.3.3 Transparency: The Alpha Channel
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# R colours are actually specified as quartets: the fourth value
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# the "Alpha channel" defines the transparency. Setting this to
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