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First minor updates 2021

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hyginn
2021-09-16 00:54:29 -04:00
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plottingReference.R
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@@ -3,18 +3,19 @@
# Purpose: Reference to graphical output in R. # Purpose: Reference to graphical output in R.
# #
# #
# Version: 2.0 # Version: 2.1
# #
# Date: 2017 09 - 2020 10 # Date: 2017 09 - 2021 09
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# V 2.1 First minor updates 2021
# V 2.0 Comprehensive reference with basic and advanced options based on # V 2.0 Comprehensive reference with basic and advanced options based on
# an integrated yeast gene expression dataset. Full rewrite of most # an integrated yeast gene expression dataset. Full rewrite of most
# sections. # sections.
# V 1.1 Stylistic improvements, code polish, and additional examples # V 1.1 Stylistic improvements, code polish, and additional examples
# V 1.0 Digest from "plotting reference" files # V 1.0 Digest from "plotting reference" files
# #
# ToDo: # ToDo: Demo 6.3.2 in parallel plots
# #
# #
@@ -22,44 +23,45 @@
#TOC> ========================================================================== #TOC> ==========================================================================
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ------------------------------------------------------------------ #TOC> -------------------------------------------------------------------
#TOC> 01 INITIALIZE 67 #TOC> 01 INITIALIZE 69
#TOC> 02 THIS REFERENCE ... 72 #TOC> 02 THIS REFERENCE ... 74
#TOC> 02.1 Dataset Documentation 79 #TOC> 02.1 Dataset Documentation 81
#TOC> 03 PROPORTIONS AND DISTRIBUTIONS 191 #TOC> 03 PROPORTIONS AND DISTRIBUTIONS 193
#TOC> 03.1 barplot() 196 #TOC> 03.1 barplot() 198
#TOC> 03.2 pie() 220 #TOC> 03.2 pie() 222
#TOC> 03.3 boxplot() 252 #TOC> 03.3 boxplot() 254
#TOC> 03.4 hist() 310 #TOC> 03.4 hist() 312
#TOC> 03.4.1 overlaying histograms 355 #TOC> 03.4.1 overlaying histograms 357
#TOC> 04 THE plot() FUNCTION 398 #TOC> 04 THE plot() FUNCTION 400
#TOC> 04.1 line plots 402 #TOC> 04.1 line plots 404
#TOC> 05 ENCODING INFORMATION: SYMBOL, SIZE, COLOR 501 #TOC> 05 ENCODING INFORMATION: SYMBOL, SIZE, COLOuR 503
#TOC> 05.1 pch ("plotting character" symbols) 507 #TOC> 05.1 pch ("plotting character" symbols) 509
#TOC> 05.1.1 Line types 682 #TOC> 05.1.1 Line types 684
#TOC> 06 COLOUR 704 #TOC> 05.2 cex ("character expansion" size) 708
#TOC> 06.1 Colours by number 712 #TOC> 06 COLOUR 768
#TOC> 06.2 Colours by name 730 #TOC> 06.1 Colours by number 776
#TOC> 06.3 Colours as hex-triplets 756 #TOC> 06.2 Colours by name 794
#TOC> 06.3.1 Inbuilt palettes 811 #TOC> 06.3 Colours as hex-triplets 820
#TOC> 06.3.2 Custom palettes 887 #TOC> 06.3.1 Inbuilt palettes 875
#TOC> 06.3.3 Transparency: The Alpha Channel 937 #TOC> 06.3.2 Custom palettes 952
#TOC> 06.4 abline(), lines() and segments() 983 #TOC> 06.3.3 Transparency: The Alpha Channel 1002
#TOC> 07 AXES 1017 #TOC> 06.4 abline(), lines() and segments() 1047
#TOC> 08 LEGENDS 1054 #TOC> 07 AXES 1081
#TOC> 08.1 basic legends 1057 #TOC> 08 LEGENDS 1118
#TOC> 08.2 Color bars 1061 #TOC> 08.1 basic legends 1121
#TOC> 09 LAYOUT 1180 #TOC> 08.2 Color bars 1125
#TOC> 10 TEXT 1215 #TOC> 09 LAYOUT 1246
#TOC> 11 DRAWING ON PLOTS 1243 #TOC> 10 TEXT 1281
#TOC> 12 IMAGES 1310 #TOC> 11 DRAWING ON PLOTS 1309
#TOC> 13 CONTOUR LINES 1315 #TOC> 12 IMAGES 1376
#TOC> 14 3D PLOTS 1320 #TOC> 13 CONTOUR LINES 1381
#TOC> 15 GRAPHS AND NETWORKS 1325 #TOC> 14 3D PLOTS 1386
#TOC> 16 OTHER GRPAHICS PACKAGES 1330 #TOC> 15 GRAPHS AND NETWORKS 1391
#TOC> 17 INTERACTIVE PLOTS 1354 #TOC> 16 OTHER GRPAHICS PACKAGES 1396
#TOC> 17.1 locator() 1358 #TOC> 17 INTERACTIVE PLOTS 1420
#TOC> 17.2 plotly:: 1361 #TOC> 17.1 locator() 1424
#TOC> 17.2 plotly:: 1427
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@@ -703,7 +705,7 @@ for (i in 1:10) {
# == 05.1 cex ("character expansion" size) ============================= # == 05.2 cex ("character expansion" size) =================================
# The size of characters can be controlled with the cex parameter. cex takes a # The size of characters can be controlled with the cex parameter. cex takes a
# vector of numbers, mapped to the vecors of plotted elements. The usual R # vector of numbers, mapped to the vecors of plotted elements. The usual R