NEWS

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EnrichedHeatmap 1.21.3

• set limit for smoothing.

EnrichedHeatmap 1.21.1

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

EnrichedHeatmap 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'

EnrichedHeatmap 1.11.1

• add 'as.normalizedMatrix()' function to convert a matrix to 'normalizedMatrix' class

EnrichedHeatmap 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

EnrichedHeatmap 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

EnrichedHeatmap 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)

EnrichedHeatmap 1.5.1

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

EnrichedHeatmap 1.3.5

• anno_enriched(): add 'abs_mean' and 'abs_sum' for 'value' argument

EnrichedHeatmap 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.

EnrichedHeatmap 1.1.8

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

EnrichedHeatmap 1.1.7

• add legends by Legend() function in the vignette

EnrichedHeatmap 1.1.5

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

EnrichedHeatmap 1.1.4

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

EnrichedHeatmap 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

EnrichedHeatmap 1.1.2

• 'normalizeToMatrix()': more options can be passed to 'locfit::locfit()'
• 'anno_enrich()': exclude NA values

EnrichedHeatmap 1.1.1

• add 'getSignalsFromList()' which summarize signals from a list of matrix
• export 'copyAttr()'

EnrichedHeatmap 0.99.3

• 'anno_enrich': get rid of lazy loading
• smoothing by locfit

EnrichedHeatmap 0.99.2

• NULL can be added to the heatmap list

EnrichedHeatmap 0.99.1

• correctly use 'system.file()' now

EnrichedHeatmap 0.99.0

• first release