版本变化测试盒框-固定plot_region_heatmap()生产时错误的情节因素是用于染色体。——固定nanopolish f5c进口位置1。-固定破碎的样品()NanoMethResults setter。——添加plot_agg_genes()函数作为plot_agg_regions速记(x, exons_to_genes(外显子(x)))。——添加能够中断methy_to_bsseq()调用。——添加处理filter_methy NanoMethResults对象()。如果使用NanoMethResult作为输入,然后NanoMethResult无形作为输出返回。注释,添加黑色轮廓外显子区相邻段串联重复序列等功能。——添加plot_gene line_size参数(),plot_region()和plot_granges()块调整大小。——添加子样品参数的热图情节,默认50。 This reduces the number of rows shown the plot to the specified amount. - Added get_exons_mm10(), get_exons_hg19(), and get_exons_hg38() as replacements for get_exons_mus_musculus() and get_exons_homo_sapiens(). - Changed heatmaps to no longer plot samples that are absent from sample annotations. - Changed heatmap labels to appear on the right rather than on top. - Changed heatmap alpha from 0.33 to 0.5. - Changed arrows in exon connectors to appear in the middle as open arrow instead of at the end as closed arrow. - Changed default X axis labels to be rescaled to appropriate SI-style. e.g. Kb, Mb, Gb. Changes in version 2.2.0 - Added heatmap argument to plot_gene(), plot_region() and plot_granges(). This adds a read-heatmap to the plot. - Added cluster_regions() function to perform k-means clustering on a table of genomic regions based on methylation profile. - Added median averaging method for trends in plot_gene(), plot_region() and plot_granges(). This can be changed using the new avg_method argument, default is mean. - Added filter_methy() function to create a filtered methylation file. - Added region_methy_stats() to obtain average methylation fractions of specific regions. - Added methy_to_edger() direct conversion wrapper around methy_to_bsseq() and bsseq_to_edger(). - Added palette argument to plot_gene(), plot_region() and plot_granges() to allow custom colour palettes. - Fixed bsseq_to_edger() failing when regions argument was used. - Fixed heatmaps not staying in a single column when more than 2 groups were present. Changes in version 2.0.0 - Major changes to plot_agg_regions(). - Features of plot_agg_regions() and plot_agg_regions_sample_grouped() merged into one interface. - Regions now specified using single table. - Changed plot_regions() default window proportion to 0. - Changed default theme from theme_bw() to theme_tufte(). - Added Megalodon data import instructions to "Importing Data" vignette. - Added scico palette defaults for heatmaps. These are colourblind friendly. - Added check for 0 length queries which would cause program to hang indefinitely. - Added setters for NanoMethResult attributes methy, samples and exons. - Added MDS and PCA plots. - Added vignette for using external annotation and dimensionality reduction. - Added binary thresholding for plot_gene(), plot_region() and plot_agg_regions(). - Added regions argument to bsseq_to_edger() to calculate aggregate counts over features rather than per site. Changes in version 1.1.4 - Added palette argument to aggregate plots - Added exons_to_genes() function to convert exon annotation to gene annotation - Added plot_granges_heatmap() function to use GRanges for plotting heatmaps Changes in version 1.1.3 - Fixed group handling for list region input in plot_agg_regions() - Fixed unused window size argument in plot_region_heatmap() - Fixed error when reads overlap in name and position for internal function StatLM() Changes in version 1.1.2 - Changed example dataset exon annotations from all genomic exons to just those contained in data. - Fixed methylation heatmap to no longer be hard coded for Peg3. - Added plot_region_heatmap() as analogue to plot_region(). - Fixed plot_agg_regions_sample_grouped() to use group column of NanoMethViz::samples(x) rather than haplotype. - Added unit tests. Changes in version 1.1.1 - Added methylation heatmap via plot_gene_heatmap(). - Fixed gene_anno() in plot_gene() for argument so FALSE actually turns off gene annotation. - Added warning for cpp11 versions <0.2.5 which may cause memory crashes when trying to import methylation data. - Added cpp11 version dependency to address tidyverse/readr#1145. - Added query methylation by gene using query_methy_gene(). Changes in version 1.0.0 - Initial Bioconductor release.