
heatmaply 1.1.1 (2020-08-20)
===============
## BUGFIX
- Cellnote did not work when using point size mapping.
- `point_size_mat` did not work when `plot_method="plotly"`
- RowSideColors/ColSideColors used default colour mapping
- showticklabels did not function as expected for ggheatmap.
- showticklabels did not function as expected when of length 1.
- Remove "\link[d3heatmap]{d3heatmap}" from .Rd since d3heatmap was removed from CRAN
- Fix "Found the following (possibly) invalid URLs:"

heatmaply 1.1.0 (2020-03-27)
===============

## NEW FEATURE
* heatmaply
  - Add dendrogram_layers argument to allow users to arbitrarily customise
    dendrograms using ggplot2 themes/scales etc before conversion to plotly
    objects.
  - Add colorbar_thickness argument to control colorbar width/thickness.
    Only effective when plot_method="plotly"

## BUGFIX
- heatmaply
  - Correctly hide dendrogram axes when plot_method="plotly"
- Make behaviour match docs for custom_hovertext when plot_method="plotly" (#231)

### OTHER NOTES
- Improve the README with link to stackoverflow.
- Updated pkgdown


heatmaply 1.0.0 (2019-12-05)
===============

## NEW FEATURES
* heatmaply
  - The argument show_dendrogram controls whether to display the row and
    column dendrograms. This allows the user to display a clustered heatmap
    without displaying the dendrograms used to cluster the data.
  - Setting hclust_method=NA uses dendextend::find_dend to find the "optimal"
    dendrogram. For details see `?find_dend`
  - Updated the vignettes with better code examples, larger figure sizes,
    and new features.
  - Add the sidecolor_colorbar_len argument to control the size of the side
    color plot legend when `plot_method = "plotly"`

## BUGFIXES
* heatmaply
  - Legends are no longer shown for the row/column dendrogram traces when
    plot_method = "ggplot".
  - cellnote would be placed outwith the heatmap when plot_method = "ggplot"
  - showticklabels applies when row_dend_left=TRUE and plot_method="plotly"
  - fontsize_row and fontsize_col apply to side colour plots as well
    as the main plot axes.
  - cellnote did not work properly in some cases.
  - grid_gap now works for side colour plots with plot_method="plotly".
  - Fixed a few canonical URL issues in the vignette

### OTHER NOTES
- Started using pkgdown :)

heatmaply 0.16.0 (2019-05-10)
===============

## NEW FEATURES
* heatmaply
  - The boolean argument dend_hoverinfo can control whether hoverinfo is shown
    for the row and column dendrograms.
## BUGFIXES
* heatmaply
  - Supplying label_names could cause incorrect orientation of side colors
  - Using plot_method="plotly" could cause incorrect interpretation of colour
    strings.
  - custom_hovertext did not work when plot_method="plotly"
  - Remove collaborate option internally (would cause warnings to be issued)
## NOTES
* heatmaply
  - Use `plotly::orca` for saving to file, rather than `plotly::export`
* Alan O'Callaghan is now recognized in the DESCRIPTION as a co-author of the package, in recognition to his significant (continuous) contribution to the package and the community. Thanks for everything Alan!

heatmaply 0.15.2 (2018-07-06)
===============

## BUGFIXES
* heatmaply
  - labels did not show (only numbers)


heatmaply 0.15.0 (2018-06-23)
===============

## NEW FEATURES
* heatmaply
  - Side colour plot legends will now have the title of the column when there is only one column used.
## BUGFIXES
* heatmaply
  - heatmaply would scramble rownames when manually supplied via labrow or labcol
  - Minor bugfixes relating to the use of the `node_size_mat` argument.
  - handle cases with row/col names are not all unique. fix #155
  - resolve some test errors.


heatmaply 0.14.1 (2018-02-01)
================

### BUGFIXES
* heatmaply
  - hover text didn't show sometimes.
  - If `custom_hovertext` is not a matrix - it is turned into a matrix (important if inserting a data.frame). Fix issue #151



heatmaply 0.14.0 (2018-01-20)
================

### NEW FEATURES
* heatmaply
  - Add `custom_hovertext` argument, adding custom hovertext option
  - Add `label_format_fun` argument, which formats text before adding to
    hovertext
  - Row and column annotation legends are now ordered according to factor
    levels, or by default, are sorted (the previous default behavior).
  - Add `node_type argument, which allows users to plot the heatmap with
    discs rather than squares. See also the `point_size_mat` argument.
  - Add `point_size_mat` argument, which is mapped to point size when
    `node_type="scatter"`. Also adds `point_size_name` argument, which is the
    name of this parameter in the heatmap hovertext.

### BUGFIXES
* heatmaply
  - Fixed a bug where column/row annotation
    legend labels would overlap when only two levels were present.

### NOTES

* Using stylr to improve the readability of the R code.
* Using devtools::spell_check() to spell check the doc.



heatmaply 0.13.0 (2017-11-11)
================

### NEW FEATURES
* heatmaply
  - Add File size arguments (#114) - width / height
  - Allows use of Pearson, Spearman or Kendall correlation
    coefficient as a distance measure, by specifying
    `distfun="pearson"`, `distfun="spearman"` or `distfun="kendall"`.
    This corresponds to the use of `distfun=function(x) as.dist(1 - cor(x)))`.



### BUG FIXES
* heatmaply
  - Scale before clustering #112 (fixes: Allow the dendrogram to use scaled data #111 )
  - stops heatmaply from crashing when using RGui (#121)
  - draw_cellnote = TRUE fails for matrix with NA (#123)






heatmaply 0.12.1 (2017-10-25)
================
### BUG FIXES
* heatmaply
  - removing tick labels with `showticklabels` now removes the ticks as
    well as the tick labels.
  - Prevent grid_gap warning (#105)
  - Add `cellnote_size` argument, controlling the font size of the cellnote.


* ggplot_heatmap
  - now handles data.frame input

### NOTES

* Added citation to the bioinformatics article! (http://dx.doi.org/10.1093/bioinformatics/btx657)



heatmaply 0.11.1 (2017-09-27)
================

### NEW FEATURES
* heatmaply
  - `side_color_layers` argument, which allows the user to pass in ggplot functions which will be
    added to the side color plots.
  - `row_side_palette` and `col_side_palette` can now be named vectors of
    colors.
  - Improved test coverage.
  - Side color plots have better defaults colors, courtesy of RColorBrewer's qualitative color palettes.
  - file argument can now work with static file extensions such as png/jpeg/pdf (thanks to the webshot package). It is also now vectorized, allowing to pass things like: heatmaply(x, file = c("heatmaply_plot.html", "heatmaply_plot.png"))
  - added labRow, labCol - to stay backward compatible with gplots::heatmap.2

### BUG FIXES
* heatmaply
  - Improved side color plots when `plot_method = "plotly"`, including improved positioning of legends.
  - grid_gap works when `plot_method = "plotly"`
  - file argument will now deal with names that includes folder names before the file name.
  - `heatmaply.heatmapr()` previously ignored `row_side_colors` and `col_side_colors` when passed to `heatmapr()` (issue #94)
  - Fix the scale of cexRow/cexCol to that of fontsize_row/col



heatmaply 0.10.1 (2017-05-27)
==============================

### NEW FUNCTIONS
* cool_warm - a new divergent color pallette (from blue to red) based on Kenneth Moreland's proposal in (Diverging color maps for scientific visualization." Advances in Visual Computing (2009)), provided by the user YAK in (http://stackoverflow.com/a/44073011/256662), and which relies on code from the Rgnuplot package.

### NEW FEATURES
* heatmaply
	- Add "auto" cellnote colouring, which predicts the luminosity of cells and switches between black and white text as 	       appropriate, for readability
	- Add `cellnote_textposition` argument, which controls the justification of cellnote within a cell.
	  See [the plotly documentation](https://plotly.com/javascript/reference/#scatter-textposition) for more details.
  - dendrogram parameter can now accept TRUE/FALSE as synonyms for "both"/"none".
	- showticklabels = c(TRUE, TRUE) - a 2d parameter to allow turning off of tick labels in the rows/columns - thus making the rendering of the plot much faster for larger matrix.
* heatmaply_cor now uses cool_warm instead of RdBu.
* Added a warning for when not using the latest ggplot version.

### BUG FIXES
* heatmaply
	- `cellnote` would previously not work with character matrices. This is now fixed.
	- heatmaply would formerly ignore colour functions when plot_method = "plotly"




heatmaply 0.9.2 (2017-05-05)
==============================

### BUG FIXES
* `heatmaply`
  * Fix subplot_width/subplot_height



heatmaply 0.9.1 (2017-04-14)
==============================

This release adds unit testing and code coverage to the heatmaply package.
Users should not be affected, but this will hopefully accelerate development
and reduce the occurrence of bugs.

### NEW FUNCTIONS
* heatmaply_na, heatmaply_cor - wrappers for heatmaply for exploring missing values patterns, and for correlation matrix.

### NEW FEATURES
* `heatmaply` -
    * Use slightly more sensible default for heights (in line with widths in any case),
      and add `subplot_widths` and `subplot_heights` arguments for user customisation.
    * `plot_method` argument ("plotly" or "ggplot") which controls the underlying
      plot method used for dendrograms and the main heatmap.
      Currently there is some disparity between the features
      available in both methods but it is hoped this can be addressed.
      plotly will likely give higher performance for large matrices.
    * Row names of matrix are now shown when `plot_method = "plotly".
      This functionality should also be added to the function when
      `plot_method = "ggplot"`, once changes are made to the plotly R package.
    * Add `colorbar_len` argument, which controls the fraction of the total height
      which the colorbar/color legend will take up.
    * Add colorbar_xpos, colorbar_ypos, to change the x and y position
      of the colorbar, in case the defaults are not suitable.
    * Add `colorbar_xanchor`, `colorbar_yanchor` arguments which control
      the anchoring points of the colorbar, relative to which the x and y position
      is applied ("left", "middle" and "right" for `colorbar_xanchor`,
      and "top", "middle" or "bottom" for `colorbar_yanchor`).
    * Allow for colorbar and side color legends to be displayed simultaneously
      when `plot_method = "plotly"`
    * Add `long_data` argumnet, which allows the user to use data in "long"
      format (eg, http://www.theanalysisfactor.com/wide-and-long-data/).
    * Add `label_names` argument, which allows the user to specify names to
      replace "row" and "column" as the names of the mouseover co-ordinates.
    * Add "cellnote" functionality, allowing the display of text overlaid
      on the cells of the heatmap. Controlled by the `draw_cellnote` argument.
      Cellnote color can be controlled by the `cellnote_color` argument.
      It is hoped that with future versions of plotly, an outline can be added,
      in order to make text readable on any background.
    * Add `fontsize_row` and `fontsize_col` arguments to heatmaply,
      which control font size for row and column labels. `cexRow` and `cexCol` are
      aliases (in order to keep compatability with gplots::heatmap.2).
    * Add `grid_gap` argument. Default is 0, higher numbers influence the gap between cells,
      helping the user to identify distinct values/cells within the matrix.
* `heatmapr`
    * Removed some unused arguments and code.
* `is.plotly` - new function to check if an object is of class plotly or not.

### BUG FIXES
* `heatmaply`
  * Fix the `cexRow` and `cexCol` arguments, which were previously non-functional.
  * Fix a mistake in an object's check in ggplot_heatmap. Props to Hannes Becker
    (https://twitter.com/SportsTribution/status/846764290484944896).
    The following no longer crashes heatmaply:
        library(heatmaply)
        df <- data.frame(1)
        heatmaply(mtcars)
  * Make sure limits work when NA are present.
  * Fix the error: "argument * matches multiple formal arguments" by adding
    an explicit "col" argument to heatmaply.


### DOCS
* heatmaply
  * Added scale and na.rm arguments to the document.
  * Added seriate.
* Cross-ref percentize and normalize.
* Vignette
  * Re-organize sections
  * Adding a section on data transformation.
  * Fixing typos



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:
==============================
* remove unneeded code from d3heatmap
* add many options for controlling the heatmap "as it should be"
* implement all relevant options streight to heatmaply.
* Expose widths and heights from heatmap_subplot_from_ggplotly to heatmaply
* write example for using seriation+dendextend for heatmaps.
* 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 :)









