heatmaply 0.8.2 (2017-03-20)
==============================


### BUG FIXES
* Remove temp files.
* Fix missing import and two typos.


heatmaply 0.8.0 (2017-03-18)
==============================

### NEW FEATURES
* heatmaply -
      * file parameter - allows to save a heatmaply plot as an HTML file.
      * Allow Rowv/Colv to also work for hclust (by turning them into a dendrogram).
      * Add examples to heatmaply's Rd and the vignette on using Rowv/Colv.
      * Added the parameters hclust_method, dist_method to allow a more refined control over dist and hclust functions which are creating the dendrograms. A user wanting an even more refined control should just supply dendrograms directly to Rowv and Colv.
      * Added the parameters: distfun_row, hclustfun_row, distfun_col, hclustfun_col. They allow a more refine control over the dendrograms of the rows/columns (without the user needing to create the dendrograms from scratch)
      * clean the modeBarButtons from irrelevent icons
  * RColorBrewer_colors - added colors to be available for the heatmap.
      The sequential palettes names are (less important since we have viridis):  Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd
      The diverging palettes are: BrBG PiYG PRGn PuOr RdBu RdGy RdYlBu RdYlGn Spectral




### BUG FIXES
* heatmaply -
  * make row_side_colors/col_side_colors work for vectors as well (by turning them to a data.frame). Fixes:  Error in if (dim(row_side_colors)[1] != dim(x)[1]) stop("row_side_colors and x have different numbers of rows") : argument is of length zero



heatmaply 0.7.0 (2017-01-21)
==============================

### NEW FEATURES
* heatmaply -
      * Non numeric columns are now added to `row_side_colors`, making heatmaply reasonably robust to heterogeneous data.frames.
      * main - a new parameter for setting the title of the plot.
      * the margins parameter now accepts 4 elements (previously it was only 2), for bottom, left, top (relevant for the plot's title) and right margins.
* heatmapr -
      * Allow k_row and k_col to accept NA. This will pick the number of clusters using dendextend::find_k

### NEW FUNCTIONS
* percentize - a pre-processing function for performing the Empirical Percentile Transformation on a vector or data.frame.
* normalize - a pre-processing function for adjusing the range of the variables to be from 0 to 1.
* is.na10 - Indicates which elements are missing (either 1 and 0)



heatmaply 0.6.1 (2016-11-11)
==============================

### BUG FIXES
* Allow dendrogram parameter to work again.


heatmaply 0.6.0 (2016-11-05)
==============================

### NEW FEATURES
* heatmaply -
      * added `row_side_colors` to allow non-numeric values in the sidebar of the
        heatmap, similar to RowSideColors in gplots::heatmap.2 (`RowSideColors` also
        works in heatmaply). Props goes to Alanocallaghan for his work on this.
      * added a proper `margins` parameter.
      * grid_color now works (thanks to a hack of using geom_hline and
        geom_vline instead of heom_tile(..., color) in ggplot_heatmap )
      * added branches_lwd - to control the width of the dendrograms' width.


heatmaply 0.5.0 (2016-08-04)
==============================

### NEW FEATURES
* is.heatmapr
* ggheatmap - first try. (not working well enough yet. The proportions of the elements are not good)
* heatmaply
  * key.title - a parameter to control the main title of the color key. (feature request by John Rizk)



heatmaply 0.4.0 (2016-07-15)
==============================

### NEW FEATURES
* heatmaply
  * grid_color - control the color of the heatmap grid. This is currently not working until this feature will be added by plotly.
  * hover over dendrogram now returns the height.
  * colors can now also accept a function (and will use it to produce 256 colors)
* heatmapr
  * seriate - character indicating the method of matrix sorting (default: "OLO"). This uses the seriation package.
  * srtRow, srtCol - add legacy support for these parameters (they are passed to row_text_angle and column_text_angle)
  * hide_colorbar - controls if the color bar should be hidden.
  * xlab, ylab - add titles to the x and y axis.


heatmaply 0.3.2 (2016-05-26)
==============================

### ANNOUNCMENTS
* heatmaply 0.3.2 - first CRAN release!

### BUG FIXES
* http -> https

heatmaply 0.3.1 (2016-05-26)
==============================
### BUG FIXES
* fix minor typos.

heatmaply 0.3.0 (2016-05-25)
==============================


### NEW FEATURES
* heatmaply
  * Now works with Rowv=F and Colv=F (by introducing a new un-exported function: heatmap_subplot_from_ggplotly)
  * Remove space between the heatmap and dendrograms (via: coord_cartesian(expand = FALSE)  and coord_flip(expand = FALSE))
  * Added the margin parameter (to control the distance between the heatmap and the dendrograms.)
  * Added row_text_angle and column_text_angle (with srtRow and srtCol for backward compatibility with gplots::heatmap.2). Fix #3

### BUG FIXES
* fix #2 : Error: Don't know how to add scale_fill_gradient_fun to a plot
  by moving "scale_fill_gradient_fun" after "..." (I may change this parameter's name later)


### VIGNETTE
* heatmaply now has a basic vignette.


heatmaply 0.2.1 (2016-05-23)
==============================

### BUG FIXES
* fix various import issues that caused warnings with devtools::check()


heatmaply 0.2.0 (2016-05-23)
==============================
### NEW FEATURES
* More control over colors in heatmaply via the new parameters: colours, limits, na.value, and scale_colour_gradient_fun.
* first attempts at row_dend_left (although this is not yet working.)

### BUG FIXES
* dendrograms are now presented without axes text.
* passing scale (= "row" or "column") works again.


heatmaply 0.1.0 (2016-05-14)
==============================

* First (very rough) version. It has a minimal working example, as well as MANY things to fix/tweak/adjust.




TODO:
==============================
* add bars for extra categories
* remove unneeded code from d3heatmap
* add many options for controlling the heatmap "as it should be"
* implement all relevant options streight to heatmaply.
* ggheatmap?
* Expose widths and heights from heatmap_subplot_from_ggplotly to heatmaply

* create colors from RcolorBrewer
* write example for using seriation+dendextend for heatmaps.

* add seriation to imports
* Show the following example for using seriation:



require(seriation)
require(dendextend)
# "GW", "OLO"
d <- dist(USArrests[1:15,])
dend <- as.dendrogram(hclust(d, method = "ave"))
par(mfrow = c(1,2))
plot(dend, main = "default")
# seriate(cophenetic(dend), method = "OLO", control = list(hclust = as.hclust(dend)))
# the downside in using cophenetic is that seriate has to go through running hclust all over again
# but we'll just have to accept it...
o <- seriate(d, method = "GW", control = list(hclust = as.hclust(dend)) )
get_order(o)
labels(cophenetic(dend))[get_order(o)]
d2 <- rotate(dend, order = rev(labels(d)[get_order(o)]))
plot(d2, main = "GW")

o <- seriate(d, method = "OLO", control = list(hclust = as.hclust(dend)) )
d3 <- rotate(dend, order = rev(labels(d)[get_order(o)]))

require(heatmaply)
heatmaply(USArrests[1:15,], Rowv = d2)
heatmaply(USArrests[1:15,], Rowv = d3)
heatmaply(USArrests[1:15,], Rowv = dend)

hmap(USArrests[1:15,])



identical(seriate(d, method = "OLO"),
		seriate(d, method = "OLO", control = list(hclust = as.hclust(dend)) ))
get_order(seriate(d, method = "OLO"))
get_order(seriate(d, method = "OLO", control = list(hclust = hclust(d, method = "sing")) )) # this works :)









