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NEWS
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NEWS
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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