# 1.11.12 * for ssvFetch*, input of a 0 length query GRanges is now an ERROR. # 1.11.11 * compressed large data objects to address warnings : save(obj, file="data/obj.rda", compress='xz') # 1.11.10 * improved clustering and heatmap messaging * max_rows and max_cols now applies to heatmap call upstream of clustering and independent when data is already clustered. # 1.11.9 * repaired missing elementType slot warning on older GRanges data objects # 1.11.8 * prepare_fetch_GRanges has been deprecated and prepare_fetch_GRanges_width should be used instead. * prepare_fetch_GRanges_names has been exposed and allows name seeting of query GRanges with what seqsetvis does internally. # 1.11.6 * bugfix when min_number = 0 * ssvFetchBam return_unprocessed supresses fragLens calc * ssvFetchBam & ssvFetchBamPE reutrn_unprocessed yields same variables # 1.11.5 * feature - fill_limits to ssvSignalHeatmap and ssvSignalHeatmap.ClusterBars to control fill limits * tweak - rel_widths default of 1,9 for ssvSignalHeatmap.ClusterBars * bugfix - drop removed ids from ssvSignalClustering * tweak - row and column drops are messages, not warnings. # 1.11.3 * feature - ssvSignalClustering accepts memb_table * feature - ssvSignalHeatmap.ClusterBars displays cluster bars once on the left instead of in each facet * feature - ssvSignalClustering accepts centroids instead of nclust * feature - exposed make_clustering_matrix to convert tidy data.table to wide matrix * feature - exposed add_cluster_annotation to append or insert cluster size bars beside heatmaps * feature - exposed assemble_heatmap_cluster_bars to make appending add_cluster_annotation easier # 1.11.2 * feature - added ssvFeatureUpset to support upset plots. # seqsetvis 1.9.19 * tweak - ssvConsensusOverlaps accepts 0 for min_fraction and min_number * bugfix - data.table::get no longer accepts multiple items, broke applySpline # seqsetvis 1.9.18 * feature - text_colors for ssvFeatureBars # seqsetvis 1.9.17 * bugfix - resolved unexpected strand behavior with flip_strand and target_strand interaction in ssvFetchBam. # seqsetvis 1.9.16 * improvement - ssvConsensusIntervalSets and ssvOverlapIntervalSets now pass ... params to findOverlaps. # seqsetvis 1.9.15 * fetch_bam return_unprocessed now returns all bam fields (seq etc.) * new feature - ssvConsensusIntervalSets allows consensus style overlaps, ie. more than 3 of 10 regions must be present. # seqsetvis 1.9.13 * parallelization support for easyLoad_* via n_cores argument # seqsetvis 1.9.11 * new feature - centerGrangesAtMax function for creating query GRanges centered at. signal maximum. #seqsetvis 1.9.10 * new feature - easyLoad_seacr function for loading seacr output bed files. * bugfix ssvFetchBamPE can handle ranges with no reads. # seqsetvis 1.9.9 *bugfix - levels of unique_names was not being used in ssvFetch functions # seqsetvis 1.9.5 * bugfix - for stranded bam fetch, strand sensititvity lost when overlapping features have opposing strands. * improvement - error if qgr has duplicate names/ids # seqsetvis 1.9.4 * bugfix - n_region_splits limited to length of qgr # seqsetvis 1.9.3 * new feature - improved parallelization by splitting up regions according to n_region_splits * improvement - fragLen for bam file is now calculatd once per bam file prior to any region splitting. * bugfix - stranded qgr and odd win_size causes inconsistent x values * bugfix - ssvFetch* - file_paths and file_attribs as data.table causes error. # seqsetvis 1.7.6 * improvement - added show_cluster_bars arg to ssvSignalHeatmap to suppress cluster labelling. * improvement - added force_append arg to appen_ynorm to conveinently overwrite previous normalization, # seqsetvis 1.7.5 * bugfix - update ssvSignalHeatmap for within_order_strategy compatibility * change - default within_order_strategy is now "sort" # seqsetvis 1.7.4 * bugfix - error if uniq_names factor # seqsetvis 1.7.2 * fix - ssvSignalClustering - within cluster sorting was not being applied * new feature - added within_order_strategy = c("hclust", "sort") paramter to ssvSignalClustering. # seqsetvis 1.5.3 * new feature - added skip_force_centerFix to all ssvFetch functions to accomodate retrieval of variable width regions using sample methods, i.e. exons. * new feature - added collapse_gr() and convert_collapsed_coord() functions to support maniulation of signal across exons. * getReadLength is now exported # seqsetvis 1.5.2 * improvement - ssvFetchGRanges does more than coverage now and can retrieve a qualititative attribute from supplied GRanges. Support for summary too. These changes are ideal for chromHMM states or similar. * improvement - added do_not_cap to append_ynorm to prevent capping at 1. * bugfix - ssvFetchSignal handle empty result. * bugfix - better seqlengths handling for fetchBam * FEATURE viewGrangesWin*_dt now handles qualitative attribute fields via attrib_name parameter. Default behavior unchanged. # seqsetvis 1.5.1 * FEATURE added calc_norm_factors and append_y_norm to facilitate normalization between datasets. * bugfix - apparent change in how names are used for which parameter of rtracklayer::import.bw required tweak in ssvFetchBam.single # seqsetvis 1.3.13 * FEATURE added ssvFetchBamPE to properly handle paired-end (PE) ChIP-seq and similar data. In contrast to ssvFetchBamPE read pairs in windows are identified and entire span of pair (instead of alignment location) is used for covereage calculation. * bugfix ssvFetchBam - fixed issue where PE data caused crash. * improvemnet - fragLen_calcStranded added flip_strand parameter to allow swapping of strand prior to strand cross correlation. * bugfix/cleanup in automatic sample naming, unlikely to affect anyone. # seqsetvis 1.3.8 * coding practice fixes # seqsetvis 1.3.7 * bam indexes are generated automatically * added flip_strand param to ssvFetchBam * bugfix/improvement ssvFetchBam passes ... args to ScanBamParam # seqsetvis 1.3.6 * change - when strands of qgr are negative, strands of results are swapped. x coordinates are already flipped. # seqsetvis 1.3.5 * bugfix/improvement - checks were timing out due to fragLen_calcStranded() poor performance. switched to shiftApply on Rle strategy to speed up. * FEATURE - ssvFetch accepts data.frame/table for file_paths (character still fine) to efficiently set additional attribues like metadata. * docs up to passing checks * FEATURE - ssvFetch* accept n_cores or uses option("mc.cores") to in parallel. * FEATURE - ssvFetchGRanges - retreives coverage of a list of GRanges in form parallel to existing ssvFetch*. # seqsetvis 1.1.7 * minor documenation improvement # seqsetvis 1.1.6 * ssvFeature* and ssvSignal* added return_data paramter to skip plotting and return data used. * ssvFetchBam added target_strand = "both" support # seqsetvis 1.1.5 * ssvBamFetch - added max_dupes parameter, default is Inf and shouldn't change behavior. uses .rm_dupes() internally. * bugfix: shift_anchor was causing a 1bp shift per call. * bugfix: ssvBamFetch, strand of qgr and target_strand interacted incorrectly and led to empty results for mismatches. # seqsetvis 1.1.4 * ssvBamFetch - added splice_strategy parameter to control split reads for RNA- seq data. Defaults is "none" and shouldn't change behavior. Uses .expand_cigar_dt() internally. # seqsetvis 1.1.3 * BiocManager added to suggests and vignette. # seqsetvis 1.1.2 * bugfix: viewGrangesWinSample/Summary_dt were both erroring when 0 reads were in window. * bugfix: ggplot2 2.3.0 compatibility fix in ssvSignalLinePlotAgg() * bugfix: col2hex now properly preserves character vector names * bugfix: ssvFetch now properly allows NA for fragLens to disable fragment extension * bugfix: ggellipse line_scale and color_scale were being ignored # seqsetvis 1.1.1 * bugfix: skip rtracklayer::import.bw depedent tests on Windows OS # seqsetvis 1.1.0 * seqsetvis is released! # seqsetvis 0.99.20 Impacts existing scripts * fetchWindowedBam is now ssvFetchBam.single * fetchWindowedBamList is now ssvFetchBam * fetchWindowedBigwig is now ssvFetchBigwig.single * fetchWindowedBigwigList is now ssvFetchBigwig * fetchWindowedSignalList is now ssvFetchSignal Independent addititions * anchor parameter for all fetch functions. allows strand sensitive x assignment and left or center reference point. * added viewGRangesWinSummary_dt() - allows summary statistic to be appled over windows in contrast to sampling method. allows qgr to be varying width. * renamed viewGRangesWindowed_dt() to viewGRangesWinSample_dt() # seqsetvis 0.99.18 * updated package title * updated vignette title # seqsetvis 0.99.17 * fetch functions, _dt versions removed and param return_data.table = FALSE added * refactoring to encapsulate fetch utility functions shared by bw and bam # seqsetvis 0.99.13 * added bamFetch* * refactored bwFetch* to use viewGRangesWindowed_dt, same as bamFetch* * ssvSignalClustering and Heatmap bug fixes related to hardcoded data.table variables * restructured and renamed extdata to be cleaner/more intuitive. # seqsetvis 0.99.12 * small changes to clear warning for Bioc acceptance. # seqsetvis 0.99.10 * fewer and smaller vignette figures * ggellipse exported with documentation * ssvSignalHeatmap calcs better xticks * ssvFeatureBinaryHeatmap true_color and false_color params added to allow color control * ssvFeatureVenn and Euler params unified * ssvFeatureBars has bar_color param like that of venn and euler # seqsetvis 0.99.9 * vigentte - some plots reduced in size and dpi reduced to save space. * ssvFeatureVenn and Euler refactored to use common internal ggellipse function for consistency. * ssvBinarizeHeatmap cleaned up plot output and changed default to raster_approximation = FALSE # seqsetvis 0.99.8 * fetch* now automatically calculate and apply a fixed width. * BiocFileCache used for all URL resources in vignette * vigentte uses cases for CTCF peak overlap and for chromHMM states complete # seqsetvis 0.99.7 * fixed examples error for ssvSignalLineplot * addressed BioC notes for seq_len instead of 1:x * addressed BioC notes for vapply instead of sapply # seqsetvis 0.99.5 * added easyLoad_narrowPeak() and easyLoad_broadPeak() * added ssvFactorizeMembTable() for converting membership table to factor * added movingAverage() from r cookbook * rename ssvSignalTrackplot to ssvSignalLineplot * rename bw_dt param to bw_data in all ssvSignal* functions to reflect increased argument flexibility (GRanges or data.table accepted). * expanded vignette to include more thorough overview, overview finished but need use cases. minor changes * renamed vignette to seqsetvis_overview.Rmd # seqsetvis 0.99.4 * rename overlapIntervalSets to ssvOverlapIntervalSets * improved documentation for CTCF datasets used by vignette * expanded vignette to include more thorough overview, work in progress. minor changes * added show_counts param to ssvFeatureBars # seqsetvis 0.99.3 * all fetch functions that previously returned data.table now return GRanges by default * all functions that accepted data.table now also accept GRanges and return the matching class where appropriate * magrittr pipes removed from all package code and magrittr moved to suggests from imports * misc minor changes to address reviewer comments (message instead of print, stopifnot to verify inputs, etc.) # seqsetvis 0.99.2 * Added a `NEWS.md` file to track changes to the package.