Coverage_Heatmaps_Notes.md

In jmw86069/platjam: Platform Jam, biological platform importers.

Ideas for coverage heatmap Rmarkdown

• user-defined output file
• option to use random subset of N regions
• subtraction of two signals (B-A)

• tabular input coverage_file

• file (or contrast)

• code (preferably a letter)
• panel_group - character group name used to associate multiple coverage lanes with the same settings: color_ramp, ylims, signal_ceiling. By default, color legend is shown for only the first member of each panel_group.
• color_ramp - comma-delimited colors, or name of color ramp recognized by jamba::getColorRamp(), which can be tested with jamba::showColors(jamba::getColorRamp("RdBu_r"))
• transform - character name of transformation function: "log2signed", "sqrt", "cubert", "qrt".
• signal_ceiling - numeric color maximum for the color ramp
• axis_name - character comma-delimited labels for the x-axis, usually three labels. Default uses the data encoded in the coverage file range.
• axis_name_fontsize - numeric fontsize in points
• axis_name_rot - numeric rotation angle
• column_fontsize - numeric fontsize in points
• lens - numeric adjustment to color ramp sensitivity, default lens=-2
• pos_line - 1,0 whether to draw line at the middle position
• ht_gap - numeric gap after this heatmap in "mm"
• profile_value - "mean", "sum", "abs_mean", "abs_sum"

• show_heatmap_legend - 0,1 whether to display color legend for this panel. Default shows color legend for the first panel in each panel_group when defined. # * ylims # * border # * legend_width # * trim_legend_title # * heatmap_legend_param

• yaxis range

• xaxis labels
• upstream_length,downstream_length - to override data ranges

• top_axis_side

• other arguments

• title - character overall title

• figure_height,figure_width - numeric height, width in inches. Default will use figure_height=8 cm, then width:

  • 0.8 inch per heatmap panel
  • 1.5 inch total color legends
  • 0.2 inch per value in anno_colnames

• top_anno_height - numeric height in cm

• legend_max_labels - integer maximum color legend labels, in case there are 40+ heatmaps
• hm_nrow - integer number of heatmap layout rows
• seed - numeric seed used to define "reproducible randomness"
• use_raster - 0,1 whether to convert output to rasterized image, almost always necessary and beneficial
• raster_quality - integer factor used to combine adjacent numeric matrix values prior to converting to image output. Useful when the R "magick" package is not available.
• raster_by_magick - 0,1 whether to use the R "magick" package if available.

• verbose - 0,1 whether to enable verbose output during processing, sometimes useful for troubleshooting.

• row partitioning arguments

• k_clusters - integer number of k-means clusters, which therefore enables k-means clustering.

• k_subset - integer number or comma-delimited numbers of k-means clusters to display after calling k-means clustering. This option is used as a follow-up step, for example running k-means once then re-running to zoom into one or more specific clusters.
• k_colors - character comma-delimited colors to assign to k-means clusters, in the order they appear.
• k_width - numeric width of k-means clustering annotation stripe, in "mm".
• k_method - character k-means method to use, typically: "euclidean", "correlation", but any method recognized by amap::hcluster().
• k_heatmap - integer or comma-delimited integers of the heatmap(s) to use during k-means clustering. Typically one heatmap is used for k-means clustering, then the partitioning is applied across all heatmaps.

• partition - character of colname(s) in the optional annofile to use for partitioning the heatmap rows.

• optional annotation file arguments

• annofile - filename full path to tab-delimited annotation data, whose first column should contain rownames that match rownames in the coverage matrix files, with additional columns that can be displayed alongside the coverage heatmap panels.

• anno_colnames - character colnames in annofile to be included in the left annotation beside coverage heatmap panels. When no anno_colnames are define, none are displayed... to prevent displaying 150 annotations, leaving no room to display coverage heatmaps.

• optional color file

• name:color association

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.