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