changes in version 1.21.3

* set limit for smoothing.

=================================

changes in version 1.21.1

* if the matrix is non-negative, after smoothing, negative values are reset to zero.

changes in version 1.13.1

* update the package according to the new version of ComplexHeatmap (>= 1.99.0)
* removed `EnrichedHeatmap` class and now the enriched heatmap is purely a `Heatmap` class object.
* add `flip_upstream` argument in `normalizeToMatrix()`.
* `pos_line` and `pos_line_gp` use the setting in `EnrichedHeatmap()` by default.
* `colSds` -> `matrixStats::colSds`

=================================

changes in version 1.11.1

* add `as.normalizedMatrix()` function to convert a matrix to `normalizedMatrix` class

=================================

changes in version 1.9.3

* support visualize category signals
* add `discretize()` to transform continuous matrices to discrete matrices
* add one more vignette showing the usage of categorical signals 

==================================

changes in version 1.9.2

* improvement on vignettes
* enriched_scores() directly applied to the normalized matrix
* row dendrogram is reordered by enriched scores if cluster_row is set to TRUE

==================================

changes in version 1.7.1

* show_row_names is put in the function argument list
* we don't use a position with 0 (either +1 or -1)
* add `dist_by_closeness()`
* add `extract_anno_enriched()`
* add ticks on axes
* add a new vignette (compare row ordering methods)

==================================

changes in version 1.5.1

* anno_enriched(): can visualize positive signals and negative signals separatedly
* add rbind.normalizedMatrix function

==================================

changes in version 1.3.5

* anno_enriched(): add `abs_mean` and `abs_sum` for `value` argument

===================================

changes in version 1.3.4

* add a new section in the vignette ("Use your own matrix")
* standard error is used instead of standard deviation for the annotation

===================================

chagnes in version 1.3.2

* makeMatrix(): consider when no target is overlaped to any signal.

===================================

changes in verison 1.1.8

* bug fixed that when there is no column name in a normal heatmap, axis is hidden.

===================================

changes in verison 1.1.7

* add legends by Legend() function in the vignette

===================================

changes in version 1.1.5

* `normalizeToMatrix`: modified default of `trim` to 0
* `makeMatrix`: w0 mode can deal with overlapping signals

====================================

changes in version 1.1.4

* the color of error areas is set 25% light of the color of corresponding line.
* support raster image for heatmap body

======================================

changes in version 1.1.3

* parameter name was wrong when constructin `ht@layout$graphic_fun_list`
* add `row_order` option in `EnrichedHeatmap()`
* `normalizeToMatrix()` supports self-defined smoothing function
* there can be no upstream or/and downstream in the heatmap
* smoothing function can be self-defined

========================================

changes in version 1.1.2

* `normalizeToMatrix()`: more options can be passed to `locfit::locfit()`
* `anno_enrich()`: exclude NA values

=========================================

changes in version 1.1.1

* add `getSignalsFromList()` which summarize signals from a list
  of matrix
* export `copyAttr()`

==========================================

changes in version 0.99.3

* `anno_enrich`: get rid of lazy loading
* smoothing by locfit

==========================================

changes in version 0.99.2

* NULL can be added to the heatmap list

===========================================

changes in version 0.99.1

* correctly use `system.file()` now

============================================

changes in version 0.99.0

* first release
 
