- ggheatmap now accepts
hide_colorbarargument. Also, whenrow_dend_leftis set toTRUE, the subplot widths are correctly reversed. (Credit jaehyunjoo, PR #273)
- Fix bug with handling of point size matrix in plotly See github issue #266
- Changed order of hovertext when plot_method="plotly" to match ggplot equivalent
- update startup message to include stackoverflow.
- add github actions (GHA)
- heatmaply wasn't printing properly in rmarkdown. Reverted back the new print method, and now it's working fine (but we get back the warning message from issue #226: talgalili#226 )
- added warning = FALSE to vignette, to make it cleaner.
- Fix incorrect use of distfun_row and hclustfun_row #254
- remove d3heatmap links from Rd
- fix issue #226 by creting print.heatmaply function to enable us to supresswarning. This is a hack, and if talgalili#226 will get resolved - then this should probably be reverted.
- Update README to include information how to port d3heatmap functions
- vignette: eval=F for some examples (so to reduce file size)
- Cellnote did not work when using point size mapping.
point_size_matdid not work whenplot_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
- 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"
- heatmaply
- Correctly hide dendrogram axes when plot_method="plotly"
- Make behaviour match docs for custom_hovertext when plot_method="plotly" (#231)
- Improve the README with link to stackoverflow.
- Updated pkgdown
- 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"
- 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
- Started using pkgdown :)
- heatmaply
- The boolean argument dend_hoverinfo can control whether hoverinfo is shown for the row and column dendrograms.
- 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)
- heatmaply
- Use
plotly::orcafor saving to file, rather thanplotly::export
- Use
- 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
- labels did not show (only numbers)
- heatmaply
- Side colour plot legends will now have the title of the column when there is only one column used.
- heatmaply
- heatmaply would scramble rownames when manually supplied via labrow or labcol
- Minor bugfixes relating to the use of the
node_size_matargument. - handle cases with row/col names are not all unique. fix #155
- resolve some test errors.
- heatmaply
- hover text didn't show sometimes.
- If
custom_hovertextis not a matrix - it is turned into a matrix (important if inserting a data.frame). Fix issue #151
- heatmaply
- Add
custom_hovertextargument, adding custom hovertext option - Add
label_format_funargument, 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 thepoint_size_mat` argument. - Add
point_size_matargument, which is mapped to point size whennode_type="scatter". Also addspoint_size_nameargument, which is the name of this parameter in the heatmap hovertext.
- Add
- heatmaply
- Fixed a bug where column/row annotation legend labels would overlap when only two levels were present.
- Using stylr to improve the readability of the R code.
- Using devtools::spell_check() to spell check the doc.
- 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"ordistfun="kendall". This corresponds to the use ofdistfun=function(x) as.dist(1 - cor(x))).
- 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
- removing tick labels with
showticklabelsnow removes the ticks as well as the tick labels. - Prevent grid_gap warning (#105)
- Add
cellnote_sizeargument, controlling the font size of the cellnote.
- removing tick labels with
-
ggplot_heatmap
- now handles data.frame input
- Added citation to the bioinformatics article! (http://dx.doi.org/10.1093/bioinformatics/btx657)
- heatmaply
side_color_layersargument, which allows the user to pass in ggplot functions which will be added to the side color plots.row_side_paletteandcol_side_palettecan 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
- 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 ignoredrow_side_colorsandcol_side_colorswhen passed toheatmapr()(issue #94)- Fix the scale of cexRow/cexCol to that of fontsize_row/col
- Improved side color plots when
- 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.
- heatmaply
- Add "auto" cellnote colouring, which predicts the luminosity of cells and switches between black and white text as appropriate, for readability
- Add
cellnote_textpositionargument, which controls the justification of cellnote within a cell. See the plotly documentation 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.
- heatmaply
cellnotewould previously not work with character matrices. This is now fixed.- heatmaply would formerly ignore colour functions when plot_method = "plotly"
heatmaply- Fix subplot_width/subplot_height
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.
- heatmaply_na, heatmaply_cor - wrappers for heatmaply for exploring missing values patterns, and for correlation matrix.
heatmaply-- Use slightly more sensible default for heights (in line with widths in any case),
and add
subplot_widthsandsubplot_heightsarguments for user customisation. plot_methodargument ("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 whenplot_method = "ggplot"`, once changes are made to the plotly R package. - Add
colorbar_lenargument, 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_yanchorarguments which control the anchoring points of the colorbar, relative to which the x and y position is applied ("left", "middle" and "right" forcolorbar_xanchor, and "top", "middle" or "bottom" forcolorbar_yanchor). - Allow for colorbar and side color legends to be displayed simultaneously
when
plot_method = "plotly" - Add
long_dataargumnet, which allows the user to use data in "long" format (eg, http://www.theanalysisfactor.com/wide-and-long-data/). - Add
label_namesargument, 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_cellnoteargument. Cellnote color can be controlled by thecellnote_colorargument. 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_rowandfontsize_colarguments to heatmaply, which control font size for row and column labels.cexRowandcexColare aliases (in order to keep compatability with gplots::heatmap.2). - Add
grid_gapargument. Default is 0, higher numbers influence the gap between cells, helping the user to identify distinct values/cells within the matrix.
- Use slightly more sensible default for heights (in line with widths in any case),
and add
heatmapr- Removed some unused arguments and code.
is.plotly- new function to check if an object is of class plotly or not.
heatmaply- Fix the
cexRowandcexColarguments, 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.
- Fix the
- 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
- Remove temp files.
- Fix missing import and two typos.
- 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
- 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 -
* 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
- 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)
- Allow dendrogram parameter to work again.
- heatmaply -
* added
row_side_colorsto allow non-numeric values in the sidebar of the heatmap, similar to RowSideColors in gplots::heatmap.2 (RowSideColorsalso works in heatmaply). Props goes to Alanocallaghan for his work on this. * added a propermarginsparameter. * 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.
- 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
- 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 - first CRAN release!
- http -> https
- fix minor typos.
- 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
- 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)
- heatmaply now has a basic vignette.
- fix various import issues that caused warnings with devtools::check()
- 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.)
- dendrograms are now presented without axes text.
- passing scale (= "row" or "column") works again.
- First (very rough) version. It has a minimal working example, as well as MANY things to fix/tweak/adjust.
- 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)
d <- dist(USArrests[1:15,]) dend <- as.dendrogram(hclust(d, method = "ave")) par(mfrow = c(1,2)) plot(dend, main = "default")
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 :)