# 1.27.2 * centerGRangesAtMax now supports view_size in the same way as other center functions # 1.27.1 * Providing unique_names as a factor to ssvFetchSignal was causing mismatches between names and input order # 1.25.5 * within_clust_sort now respects "none" sort strategy. was bugged # 1.25.4 * applyMovingAverage should handle extra columns better now # 1.25.3 * ssvFetchBamPE.RNA now uses anchor = "left" internally # 1.23.14 * reimplemneted "left" and "right" within_cluster_sort_strategy for ssvSignalClustering # 1.23.13 * added ssvAnnotateSubjectGRanges to add mcols from overlapping GRanges to subject * ssvOverlapIntervalSets and ssvConsensusIntervalSets now have preserve_mcols flag to automatically apply ssvAnnotateSubjectGRanges # 1.23.11 * make_facet_str - to handle facets # 1.23.9 * fixed mis behaving test # 1.23.7 * bugfix for emergent ggplot2 conflict using palette in banded quantile plots # 1.23.6 * bugfix for 1.23.5 fix where query width < 1/2 window size for summary # 1.23.5 * bugfix to handle edge case of query width less than window size for summary # 1.23.4 * bugfix for previous bugfix - easyLoad_FUN was failing when source file was empty * bugfix for "center" anchor. Uses shifted result of same code as "left" now. # 1.23.3 * bugfix - easyLoad_bed (and specifically easyLoad_seacr) now assign unique values of `name` as default. # 1.23.2 * bigfix - heatmaps generated with min_method = "summary" had inappropriate cluster bar spacing. # 1.23.1 * BUGFIX for splice_strategy = "splice_count" soft clippped reads would improperly shift position by 1. # 1.21.13 * ssvMakeMembTable now tolerates NA values with a warning. # 1.21.12 * safeBrew accepts logical as n # 1.21.11 * bugfix where centerGRangesAtMax was not passing x_ to centerAtMax # 1.21.10 * added gg/ggplot/ggplot2 pal to safeBrew to reproduce ggplot default colors # 1.21.9 * added applyMovingAverage equivalent of applySpline # 1.21.7 * rm bad file in test causing bioc error # 1.21.6 * splice_count target_strand and flip_strand now behaves consistently and is tested # 1.21.5 * bugfix for flip_strand when splice_strategy == "splice_count", was not being applied # 1.21.4 * bugfix for assembling more than 2 heatmap elements, now nrow = 1 # 1.21.3 * added do_not_scaleTo1 to append_ynorm. # 1.21.2 * added findMaxPos # 1.21.1 * added counts_as_percent and percentage_digits to ssvFeatureVenn to allow percentages to be displayed # 1.19.4 * added count_label_size = 8 to ssvFeatureBars # 1.19.3 * bugifx: ssvSignalLineplotAgg now uses non-default values of y_ properly # 1.19.2 * Update all aes_string calls to aes with tidy ideoms to avoid deprecated aes_string * Use linewidth instead of size to avoid deprecated use of size # 1.19.1 * Catch up devel to recent development # 1.18.1 * Catch up release to recent development # 1.15.18 * Added named color vector support to rect_color and text_color to add_cluster_annotation. * ssvSignalHeatmap and ssvSignalHeatmap.ClusterBars both support basic add_cluster_annotation arguments. (rect_color, text_color, label_angle, show_label) # 1.15.16 * ssvSignalHeatmap, ssvSignalHeatmap.ClusterBars, and ssvSignalClustering now support fun.aggregate to combine values when facet covers multiple samples. # 1.15.15 * added certain add_cluster_annotation arguments to ssvSignalHeatmap.ClusterBars # 1.15.14 * added fragLens as a dummy argument to ssvFetchBigwig and ssvFetchBamPE to increase flexibility # 1.15.12 * minor bugfix for nclust reduction in ssvSignalClustering in for low uniqueness. # 1.15.11 * added support for empty bed and np files to easyLoad_* # 1.15.10 * ssvFetchGRanges no accepts GrangesList properly # 1.15.9 * added copy_clust_info to duplicate cluster info (row order and cluster assignment) from one ssvSignalClustering result to any ssvFetch* result. * added get_mapped_reads functiont to retrieve mamped read counts from bam files * fixed data.table shallow copy warning in within_clust_order # 1.15.7 * safeBrew now accepts character and factor inputs and returns named colors accordingly. * ssvSignalHeatmap.ClusterBars refined annotation bar placement # 1.15.6 * bugfix, needed explicit GenomeInfoDb::seqlevels # 1.15.5 * cowplot added to imports * bugfixes with seqlevels in view functions(Bioc 15 new). # 1.15.3 * build warning fix - didn't update docs when changing raster_approximation default for ssvBinaryHeatmap # 1.15.2 * default for ssvFeatureBinaryHeatmap is now raster_approximation = TRUE * optimization of ssvFactorizeMembTable # 1.14.2 * more robust seqnames handling in harmonize_seqlengths with user instruction to resolve issues. * bugfix for seqlengths in fetch_bamPE # 1.14.1 * bugfix for "invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not identical" # 1.13.10 * bugfix fixed bad example in clusteringKmeansNestedHclust # 1.13.8 * added "reverse" within_order_strategy options to within_clust_sort * added function reverse_clusters - reverses cluster orders * added function split_cluster - splits existing cluster up # 1.13.6 * added "left" and "right" within_order_strategy options to within_clust_sort * added function reorder_clusters_stepdown - attempts to arrange clusters so that more signal is on the left at the top and right at the bottom * added function reorder_clusters_hclust - arranges clusters using hierarchical clustering of centroids * added function reorder_clusters_manual - manually specify cluster order, brings manually specified clusters to top * added function merge_clusters - merges multiple clusters together # 1.13.5 * more robust harmonize_seqlengths # 1.13.4 * auto reduce nclust when too high # 1.13.3 * better bugfix to avoid using pbmclapply on windows via ssv_mclapply # 1.13.2 * bugfix to avoid using pbmclapply on windows # 1.13.1 * calling ssvFeatureUpset with a single set now produces plot with message instead of uncaught error. * data.table assignments by [[]] switched to set() to avoid invalid .internal.selref warnings * fragLens calc is now multicore * added easyLoad_FUN to allow arbitrary load functions * added easyLoad_IDRmerged * added within_cluster_sort for sorting within clusters by different values/data. * kmeans iter.max * inject formating to ssvSignalHeatmap.ClusterBars with FUN_format_heatmap * cluster reorder disabled if manual clusters * docs to address warnings and notes # 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.