Add the biplot man.

Author: joa-quim

documentation/modules/biplot.md

@@ -0,0 +1,68 @@
+# biplot
+
+```julia
+biplot(name::String | D::GMTDataset; arrow::Tuple=(0.3, 0.5, 0.75, "#0072BD"), cmap=:categorical,
+       colorbar::Bool=true, marker=:point,ms="auto", obsnumbers::Bool=false, PC=(1,2),
+       varlabels=:yes, xlabel="", ylabel="", kw...)
+```
+
+Create a 2D biplot of the Principal Component Analysis (PCA) of a two-dimensional chart that
+represents the relationship between the rows and columns of a table.
+
+- `cmd0`: The name of a 2D data table file readable with ``gmtread()``, or a ``GMTdataset`` with the data.
+
+- `arrow`: a tuple with the following values: (len, shape, width, color). If this default is used we scale them by fig size.
+   - `len`: the length of the arrowhead in cm. Default is 0.3.
+   - `shape`: the shape of the arrow. Default is 0.5.
+   - `width`: the width of the arrow stem in points. Default is 0.75.
+   - `color`: the color of the arrow. Default is "#0072BD".
+
+- `cmap`: a String or Symbol with the name of a GMT colormap. 
+   - Or a string with "matlab" or "distinct"
+   - Or "alphabet" for colormaps with distinct colors.
+   - Or a comma separated string with color names; either normal names ("red,green") or hex color codes ("#ff0000,#00ff00").
+   - Or "none" for plotting all points in black color. A single color in hexadecimal format plots all points in that color.
+   Default is "categorical".
+
+- `colorbar`: whether to plot a colorbar. Default is true.
+
+- `marker`: a String or Symbol with the name of a GMT marker symbol. Default is "point".
+
+- `ms`: a String or Symbol with the name of a GMT marker size. Default is "auto" (also scales sizes with the size of the plot).
+
+- `obsnumbers`: whether to plot observation numbers on the plot. Default is false. Note that in this case we are not able
+   to plot colored numbers by category, so we plot the symbols as well (use `cmap="none"` if you don't want this).
+
+- `PC`: a tuple with the principal components to plot. Default is (1, 2). For example, PC=(2,3) plots
+   the 2nd and 3rd principal components.
+
+- `varlabels`: whether to plot variable labels. The default is :yes and it prints as labels the column names
+   if the input GMTdataset. Is it hasn't column names, then it prints "A,B,C,...". Give a string vector to plot custom labels.
+
+- `xlabel`: a String with the x-axis label. Default is "", which prints "PC[PC[1]]".
+
+- `ylabel`: a String with the y-axis label. Default is "", which prints "PC[PC[2]]".
+
+- `kw...`: Any additional keyword argument to be passed to the ``plot()`` function.
+
+
+Examples
+--------
+
+See the classic analysis of the _Iris_ dataset. 
+
+\begin{examplefig}{}
+```julia
+using GMT
+biplot(TESTSDIR * "iris.dat", show=true)
+```
+\end{examplefig}
+
+Plot a 6 cm fig with the observarion numbers.
+
+\begin{examplefig}{}
+```julia
+using GMT
+biplot(TESTSDIR * "iris.dat", figsize=6, obsnumbers=true, show=true)
+```
+\end{examplefig}

documentation/utilities/binarize.md

@@ -1,25 +1,39 @@
 # binarize
 
 ```julia
-    Ibw = binarize(I::GMTimage, threshold::Int=0; band=1, , threshold::Int=0, revert=false) -> GMTimage
+    Ibw = binarize(I::GMTimage, threshold::Int=0; band=1, threshold::Int=0, revert=false, bool::Bool=false) -> GMTimage
+```
+
+---
+or
+
+```julia
+Ibw = binarize(I::GMTimage, threshold::Vector{Int}; band::Int=1, revert::Bool=false, bool::Bool=false)
 ```
 
 Convert an image to a binary image (black-and-white) using a threshold.
 
 ### Args
 - `I::GMTimage`: input image of type UInt8.
 
-- `threshold::Int`: A number in the range [0 255]. If the default (0) is kept and the keyword
+- `threshold`: A number in the range [0 255]. If the default (0) is kept and the keyword
   `threshold` is not used, then the threshold is computed using the \myreflink{isodata} method.
+   Alternatively, a vector of two numbers in the range [0 255] can be used. In this case, the
+   threshold is set to the first value and the second value is used to set the upper limit of the
+   threshold range. That is, values between the two values are set to 255 and the rest to 0
+   (or `true` and false respectively when the `bool` keyword is set to `true`). Note that with
+   this second form, the `threshold` keyword does not exist.
 
 ### Kwargs
 - `band`: If the `I` image has more than one band, use `band` to specify which one to binarize.
    By default the first band is used.
 
+- `bool`: If `true`, the output image is of type Bool, otherwise it is of type UInt8.
+
 - `threshold`: Alternative keyword argument to the positional `threshold` argument. Meaning, one can either
   use the `binarize(I, ??)` or `binarize(I, threshold=??)`.
 
-- `revert`: If `true`, values below the threshold are set to 255, and values above the threshold are set to 0.
+- `revert`: If `true`, values below the threshold are set to 255, and values >= the threshold are set to 0.
 
 ### Return
 A new \myreflink{GMTimage}.