diff --git a/plottingReference.R b/plottingReference.R index eb24f68..fb576db 100644 --- a/plottingReference.R +++ b/plottingReference.R @@ -3,64 +3,66 @@ # 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) # +# V 2.1 First minor updates 2021 # V 2.0 Comprehensive reference with basic and advanced options based on # an integrated yeast gene expression dataset. Full rewrite of most # sections. # V 1.1 Stylistic improvements, code polish, and additional examples # V 1.0 Digest from "plotting reference" files # -# ToDo: +# ToDo: Demo 6.3.2 in parallel plots # # #TOC> ========================================================================== -#TOC> -#TOC> Section Title Line -#TOC> ------------------------------------------------------------------ -#TOC> 01 INITIALIZE 67 -#TOC> 02 THIS REFERENCE ... 72 -#TOC> 02.1 Dataset Documentation 79 -#TOC> 03 PROPORTIONS AND DISTRIBUTIONS 191 -#TOC> 03.1 barplot() 196 -#TOC> 03.2 pie() 220 -#TOC> 03.3 boxplot() 252 -#TOC> 03.4 hist() 310 -#TOC> 03.4.1 overlaying histograms 355 -#TOC> 04 THE plot() FUNCTION 398 -#TOC> 04.1 line plots 402 -#TOC> 05 ENCODING INFORMATION: SYMBOL, SIZE, COLOR 501 -#TOC> 05.1 pch ("plotting character" symbols) 507 -#TOC> 05.1.1 Line types 682 -#TOC> 06 COLOUR 704 -#TOC> 06.1 Colours by number 712 -#TOC> 06.2 Colours by name 730 -#TOC> 06.3 Colours as hex-triplets 756 -#TOC> 06.3.1 Inbuilt palettes 811 -#TOC> 06.3.2 Custom palettes 887 -#TOC> 06.3.3 Transparency: The Alpha Channel 937 -#TOC> 06.4 abline(), lines() and segments() 983 -#TOC> 07 AXES 1017 -#TOC> 08 LEGENDS 1054 -#TOC> 08.1 basic legends 1057 -#TOC> 08.2 Color bars 1061 -#TOC> 09 LAYOUT 1180 -#TOC> 10 TEXT 1215 -#TOC> 11 DRAWING ON PLOTS 1243 -#TOC> 12 IMAGES 1310 -#TOC> 13 CONTOUR LINES 1315 -#TOC> 14 3D PLOTS 1320 -#TOC> 15 GRAPHS AND NETWORKS 1325 -#TOC> 16 OTHER GRPAHICS PACKAGES 1330 -#TOC> 17 INTERACTIVE PLOTS 1354 -#TOC> 17.1 locator() 1358 -#TOC> 17.2 plotly:: 1361 -#TOC> +#TOC> +#TOC> Section Title Line +#TOC> ------------------------------------------------------------------- +#TOC> 01 INITIALIZE 69 +#TOC> 02 THIS REFERENCE ... 74 +#TOC> 02.1 Dataset Documentation 81 +#TOC> 03 PROPORTIONS AND DISTRIBUTIONS 193 +#TOC> 03.1 barplot() 198 +#TOC> 03.2 pie() 222 +#TOC> 03.3 boxplot() 254 +#TOC> 03.4 hist() 312 +#TOC> 03.4.1 overlaying histograms 357 +#TOC> 04 THE plot() FUNCTION 400 +#TOC> 04.1 line plots 404 +#TOC> 05 ENCODING INFORMATION: SYMBOL, SIZE, COLOuR 503 +#TOC> 05.1 pch ("plotting character" symbols) 509 +#TOC> 05.1.1 Line types 684 +#TOC> 05.2 cex ("character expansion" size) 708 +#TOC> 06 COLOUR 768 +#TOC> 06.1 Colours by number 776 +#TOC> 06.2 Colours by name 794 +#TOC> 06.3 Colours as hex-triplets 820 +#TOC> 06.3.1 Inbuilt palettes 875 +#TOC> 06.3.2 Custom palettes 952 +#TOC> 06.3.3 Transparency: The Alpha Channel 1002 +#TOC> 06.4 abline(), lines() and segments() 1047 +#TOC> 07 AXES 1081 +#TOC> 08 LEGENDS 1118 +#TOC> 08.1 basic legends 1121 +#TOC> 08.2 Color bars 1125 +#TOC> 09 LAYOUT 1246 +#TOC> 10 TEXT 1281 +#TOC> 11 DRAWING ON PLOTS 1309 +#TOC> 12 IMAGES 1376 +#TOC> 13 CONTOUR LINES 1381 +#TOC> 14 3D PLOTS 1386 +#TOC> 15 GRAPHS AND NETWORKS 1391 +#TOC> 16 OTHER GRPAHICS PACKAGES 1396 +#TOC> 17 INTERACTIVE PLOTS 1420 +#TOC> 17.1 locator() 1424 +#TOC> 17.2 plotly:: 1427 +#TOC> #TOC> ========================================================================== @@ -352,7 +354,7 @@ hist(SC$mdl$peaks, # gene expression first peaks col = myPal(81)) # get 81 color values from myPal() -# === 03.4.1 overlaying histograms +# === 03.4.1 overlaying histograms # Histograms can be plotted one-over another to compare them # Example: when do genes with different GO term annotations first peak? @@ -679,7 +681,7 @@ legend ("bottom", box.col = "#DDDDDD", bg = "#FFFFFF") -# === 05.1.1 Line types +# === 05.1.1 Line types # Basically all plots take arguments lty to define the line type, and lwd # to define line width @@ -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 # vector of numbers, mapped to the vecors of plotted elements. The usual R @@ -870,7 +872,7 @@ N <- 40 barplot(rep(1, N), col = col2hex(myCols,pal=TRUE,N=N) ) -# === 06.3.1 Inbuilt palettes +# === 06.3.1 Inbuilt palettes # In R, a palette is a function (!) that takes a number as its argument and # returns that number of colors, those colors can then be used to color points @@ -947,7 +949,7 @@ RColorBrewer::display.brewer.all(colorblindFriendly = TRUE) plotPal(RColorBrewer::brewer.pal(11, "PuOr"), N = 11) -# === 06.3.2 Custom palettes +# === 06.3.2 Custom palettes # # Bespoke palettes are easily created with colorRampPalette(). The function # returns a palette, i.e. a function (not a vector of colors). You assign the @@ -997,7 +999,7 @@ plotPal(myOutliers) # also an option to extract palettes from user-supplied images. -# === 06.3.3 Transparency: The Alpha Channel +# === 06.3.3 Transparency: The Alpha Channel # R colours are actually specified as quartets: the fourth value # the "Alpha channel" defines the transparency. Setting this to