version 1.0.1

DESCRIPTION

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+Package: squash
+Version: 1.0.1
+Date: 2011-08-15
+Title: Color-based plots for multivariate visualization
+Author: Aron Eklund
+Maintainer: Aron Eklund <eklund+squash@cbs.dtu.dk>
+Depends: grDevices
+Description: This package provides functions for color-based
+        visualization of multivariate data, i.e. colorgrams or
+        heatmaps.  Lower-level functions are provided to map numeric
+        values to colors, display a matrix as an array of colors, and
+        draw color keys.  Higher-level plotting functions are provided
+        to generate a bivariate histogram, a dendrogram aligned with a
+        color-coded matrix, a triangular distance matrix, and more.
+License: Artistic-2.0
+URL: http://www.cbs.dtu.dk/~eklund/squash/
+Packaged: 2012-10-29 08:59:49 UTC; ripley
+Repository: CRAN
+Date/Publication: 2012-10-29 08:59:49

MD5

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+5edde01db53920785ab64fa964449afb *DESCRIPTION
+6dbf5337a68b3906b42c512850aa973c *NAMESPACE
+901118a222919be6fe3036ca95359e18 *NEWS
+df5ecd94bce28dd57ce098b2456a400d *R/distogram.R
+924597a1476cdd0f705eccde4797aa24 *R/squash.R
+4939e0848ba78f083371cc51179f2000 *man/ColorPalettes.Rd
+f7ea3726e2d458adc83260319d1ab8ef *man/cimage.Rd
+11b8be856db2849fbc8ff4c1943850ae *man/cmap.Rd
+a872f24a0494ed79599773bfdad56867 *man/colorgram.Rd
+e83e81481241ce5651dba79c2642319f *man/corrogram.Rd
+0a5616faaa5896b6e0f6d2deb15262bd *man/dendromat.Rd
+f761c12896121179aba382303b418aec *man/diamond.Rd
+1b52082a0e2e248e62a5624c8f052777 *man/distogram.Rd
+62d384871fc3fd0056da717f8c01876d *man/hist2.Rd
+ac1864eebb9c47bb398a7278481a40fd *man/hkey.Rd
+310aa50eda0769de6a794043499c2b30 *man/makecmap.Rd
+5a7eb8b7bc8ef220e793b97b1637fb92 *man/matapply.Rd
+d1dec50054bc2880f9dbaf3972808556 *man/prettyInt.Rd
+c6ceaba828c5db7b2ab8d78aef8d8c49 *man/savemat.Rd
+7a7f36999bb0a5cf9ea49ad73f52b847 *man/squashgram.Rd
+7a848b30dd989f0a1f933f3761f52cc4 *man/trianglegram.Rd
+23137457888be0df19d17511c72d44fe *man/xyzmat.coords.Rd
+a91a61521429f5efc2f235cccea0f99a *man/xyzmat2xyz.Rd

NAMESPACE

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+# Default NAMESPACE created by R
+# Remove the previous line if you edit this file
+
+# Export all names
+exportPattern(".")
+
+# Import all packages listed as Imports or Depends
+import(
+  grDevices
+)

NEWS

@@ -0,0 +1,192 @@
+Squash NEWS
+
+
+Changes in version 1.0.1 (2011-08-15)
+
+- First CRAN release
+- "hist2" now has a new argument "breaks", which defaults to "prettyInt"
+- Fixed bug in "cimage" in which axes were plotted when add=TRUE
+- Fixed bug in "makecmap" causing domain extension into positive numbers when x is all negative
+- Fixed bug in which "prettyLog" could return only a single value
+- Add check for zero-length x in "prettyInt" and "prettyLog" to match behavior of "pretty"
+- "prettyInt" now performs better when x includes all of {zero, negative numbers, positive numbers}
+- In "makecmap", the old argument "center" is now called "symm" (for symmetric)
+- "makecmap" gets a ... argument, passed to "breaks"
+- "dendromat" now ends with par(usr) set to c(0,1,0,1)) instead of something unpredictable; this should make legend placement a bit easier.
+- "dendromat" now ends by resetting the clipping region, so "vkey" can be used afterwards.
+
+
+Changes in version 1.0.0 (2011-08-11)
+
+- MAJOR update, with several function names *changed* to improve clarity; sorry for any inconvenience 
+- The previous "colormap" is now called "makecmap"
+- The previous "num2col" is now called "cmap"
+- The previous "raster" is now called "cimage"
+- The option "trueRaster" is now called "useRaster" for consistency with the standard function "image".
+- Remove the old "orangeblue"
+- The old "orangeblue2" is now "blueorange"
+- The old "darkredblue" is slightly adjusted to make the extremes distinguishable and is now called "darkbluered"
+- New color palette "bluered".
+- The old function "squash" is now called "matapply"
+- The old function "mat2bm" is now called "savemat"
+- Improvements in automatic axis naming in squashgram and matapply
+
+
+Changes in version 0.4.4 (2011-08-09)
+
+- Documentation improvements.
+- Rename "pretty.log" -> "prettyLog" to avoid S3 method warnings
+- Rename "pretty.int" -> "prettyInt"
+- Added argument "do.dev.off" to function "mat2bm"
+- 'squashgram' now uses xyz.coords, which can change the automatic axis labels
+- Some 'squash', 'squashgram', and 'hist2' parameters are now NULL by default: xlim,  ylim, xbreaks, ybreaks
+- 'raster' now takes arguments 'xlabels', 'ylabels', and 'axes'
+- Removed the mostly useless functions 'raster2' and 'colorgram2'
+
+
+Changes in version 0.4.3 (2011-02-21)
+
+- "dendromat" now looks for names in argument "x" if "labRow" is NULL.
+
+
+Changes in version 0.4.2 (2010-11-01)
+
+- Added function "raster2"; like "raster" but with categorical axes.
+- Added function "colorgram2"; like "colorgram" but with categorical axes.
+
+
+Changes in version 0.4.1 (2010-10-26)
+
+- Replace "xyz.coords.matrix" with "xyzmat.coords" and "xyzmat2xyz".
+- "raster" and "colorgram" now use "xyzmat.coords" as front end for input.
+- Fix bug in "colormap" that could cause errors when pretty.log is used with negative values.
+- Remove function "pretty.auto"
+- New argument "small" in "pretty.log"
+- "pretty.log" now deals with negative numbers
+- Fixed bug in "pretty.log" that caused it to overshoot the maximum.
+- New color palette "coolheat"
+
+
+Changes in version 0.4.0 (2010-10-21)
+
+- Several major changes!
+- Modify "raster" to optionally use the (relatively) new "rasterImage" function from "graphics" package.
+- Replace function "matpng" with new function "mat2bm", which works better and supports a few other graphics devices.
+- Added function "xyz.coords.matrix".
+- "squash" now accepts a matrix as input, using xyz.coords.matrix
+- The former "minikey2h" and "minikey2v" have been replaced by "hkey" and "vkey", which are similar but have slightly different arguments
+- Remove functions "minikey", "keyPlus", and "drawKey"
+- "colorgram" and "distogram" updated to call hkey and vkey
+- Replaced function "triplotCol" with "trianglegram", which now accepts new arguments.
+- "raster" and "colorgram" no longer accept labels (character) for x and y
+
+
+Changes in version 0.3.1 (2009-11-04) 
+
+- Added function "matpng".
+
+
+Changes in version 0.3.0 (2009-07-21)
+
+- Added function "orangeblue2"
+- Change name of "pretty.pseudolog" to "pretty.log".
+- "pretty.int" was broken in several ways, but should be fixed now.
+- Removed "pretty.count".
+- Added function "pretty.auto".
+- "colorgram" now works differently: 1. The parameter "key" now takes numeric values to specify the type of key. 2. Removed parameter "key.width".  3. Added parameter "key.args".
+
+
+Changes in version 0.2.3 (2009-07-18)
+
+- New functions "minikey2h" and "minikey2v".
+- Changed the name of this file to "NEWS" (was "ChangeLog").
+
+
+Changes in version 0.2.2 (2009-05-05)
+
+- Revert many of the changes to "colormap" made in v. 0.2.0.
+- Modified the "pretty.*" functions.
+- Removed "int" argument from "colorgram".
+- Many other fixes and updates.
+- Remove "legend.map".
+
+
+Changes in version 0.2.1 (2009-05-05)
+
+- Added arguments (xaxp, yaxp, xaxt, yaxt, bty, las) to "raster".
+- Added function "pretty.count" and "pretty.pseudolog".
+
+
+Changes in version 0.2.0 (2009-03-05)
+
+- "colormap" now returns additional list items "n", "center", "equal", "type".
+- In "colormap", "x" can be omitted if breakpoints are specified.
+- In "colormap", new parameters: "int", "col.zero".
+- "Colormap" now can do "integer-based" maps.
+- In "colormap", defaults for "right" is now TRUE, which matches the defaults for "cut".  (Originally, it was the other way around because this made more sense for integers).
+- Added helper functions "pretty.int", "integer.intervals".
+- Documentation fixes.
+- Added arguments to "dendromat":  "border", "cex.lab" (suggested by Chris Workman).
+- Added "gap" argument to "dendromat".
+- Change "triplotCol" so it only adjusts the right-hand margin by default (and not the other margins).
+
+
+Changes in version 0.1.9 (2008-12-16)
+
+- Adjust "triplotCol" such that labels fall on 1, 2, 3, ... instead of 1, 3, 5, ...
+- Remove "line" parameter from "triplotCol", add "fix.mar" parameter.
+
+
+Changes in version 0.1.8 (2008-12-12)
+
+- Minor documentation updates. 
+- Added "diamond", "distogram", "corrogram", "triplotCol", and "miniKey".
+
+
+Changes in version 0.1.7 (2008-08-05)
+
+- Added color palette "darkredblue".
+
+
+Changes in version 0.1.6 (2008-05-03)
+
+- Added function "dendromat".
+- Misc. documentation fixes.
+
+
+Changes in version 0.1.5 (2008-03-02)
+
+- Change "raster" to set up plot in normal way (i.e. with "plot"), and remove "..." argument, which was pretty much useless.
+- Update "raster" to work work with non-evenly spaced breakpoints/midpoints and non-1 zsize.
+- These changes also fix buggy behavior in raster.
+- Misc. documentation fixes.
+
+
+Changes in version 0.1.4 (2008-02-28)
+
+- Added "heat" as a new palette.
+- Added "keyPlus" function.
+- In "drawKey", changed default las.axis = 1
+
+
+Changes in version 0.1.3 (2008-02-26)
+
+- Documentation improvements.
+- "squash" now uses "xyz.coords" for input, and returns additional list items "xlab", "ylab", and "zlab".
+- Similarly, "hist2" now used "xy.coords".
+- The argument in "colorgram" formerly called "key.lab" is now called "zlab", for compatibility with "persp".  Also, "xlab" and "ylab" are specifically included in the argument list.
+- "colorgram" and "raster" now try harder to assign dimension labels.
+- "raster" is a bit more flexible with input (but still not ideal).
+
+
+Changes in version 0.1.2 (2008-02-23)
+
+- A few documentation improvements.
+- Several improvements to "drawKey":
+-  Added "digits" and "by" arguments to control axis formatting.
+-  Removed "at" argument (use "by" instead).
+-  Default "las.lab" argument is now 0.
+-  Default "las.axis" argument is now 2.
+-  "side" = 1 and "side" = 3 now work.
+-  By default (i.e., when "by" = NA), the function tries to avoid plotting axis labels on top of each other.
+

R/distogram.R

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+# distogram.R
+#
+# Aron Eklund
+#
+
+
+diamond <- function(x, y = NULL, radius, ...) {
+  xy <- xy.coords(x, y)
+  xL <- xy$x - radius
+  xC <- xy$x
+  xR <- xy$x + radius
+  yB <- xy$y - radius
+  yC <- xy$y
+  yT <- xy$y + radius
+  n <- length(xL)
+  x2 <- rbind(rep.int(NA, n), xC, xL, xC, xR)[-1]
+  y2 <- rbind(rep.int(NA, n), yB, yC, yT, yC)[-1]
+  polygon(x2, y2, ...)
+}        
+
+
+trianglegram <- function(x, labels = rownames(x), 
+    lower = TRUE, diag = FALSE, right = FALSE, 
+    add = FALSE, xpos = 0, ypos = 0, xlim, ylim, ...) {
+  if(nrow(x) != ncol(x))
+    stop("x must be a square matrix")
+  n <- nrow(x)
+  if(lower) {
+    wh <- lower.tri(x, diag = diag)
+  } else {
+    wh <- upper.tri(x, diag = diag)
+  }
+  ## x1, y1 = unrotated coordinates
+  x1 <- col(x)[wh]
+  y1 <- row(x)[wh]
+  ## rotated coordinates
+  if(right) {
+    x2 <- (  y1 - x1) / 2
+    y2 <- (x1 + y1) / 2 
+  } else {     # right
+    x2 <- (- y1 + x1) / 2
+    y2 <- (x1 + y1) / 2 
+  }
+  x2 <- x2 + xpos
+  y2 <- y2 + ypos
+  if(is.null(labels)) labels <- 1:n
+  if(!add) {
+    if(missing(xlim)) xlim <- c(-n/2, n/2) + xpos
+    if(missing(ylim)) ylim <- c(0.5, n + 0.5) + ypos
+    plot(xlim, ylim, type = 'n', 
+      axes = FALSE, xlab = '', ylab = '', ...)
+  }
+  diamond(x2, y2, radius = 0.5, col = x[wh])
+  if(diag) offset <- 0.5 else offset <- 0
+  if(right) {
+    text(0, 1:n, labels = labels, pos = 2, offset = offset, xpd = NA)
+  } else {
+    text(0, 1:n, labels = labels, pos = 4, offset = offset, xpd = NA)
+  }
+}  
+
+
+distogram <- function(x, map, n = 10, base = NA, colFn = heat,
+    key = TRUE, title = NA, ...) {
+  if(class(x) == 'dist') x <- as.matrix(x)
+  stopifnot(nrow(x) == ncol(x))
+  if (missing(map)) {
+    map <- makecmap(x, n = n, base = base, colFn = colFn)
+  }
+  trianglegram(cmap(x, map = map), ...)
+  if(key) hkey(map = map, title = title)
+  invisible(map)
+}  
+
+
+corrogram <- function(...) {
+  map <- makecmap(c(-1,1), n = 20, colFn = blueorange, include.lowest = TRUE)
+  distogram(..., map = map)
+}  
+
+