(IN DEV) Make coverage heatmaps using a simple set of config options
nmathm_row_order(HM, ...)list output from nmatlist2heatmaps() that
is expected to contain at least one list element
named "HM_drawn" or "draw", with "HM_drawn"
used first if present. Either object is also expected
to contain slotName ht_list which represents the
HeatmapList. Among the heatmaps in the HeatmapList,
the first with class "Heatmap" that is not named
"cluster" will be used, since "cluster" is the name
of the heatmap used to represent k-means or other
clustering output to partition rows.
additional arguments are ignored.
list of rownames, where each list represents one
row_slice used in the heatmap, as defined by
nmatlist2heatmaps() arguments partition or
k_clusters.
This function is still in development and is not yet active.
This function is intended as a wrapper function which calls
nmatlist2heatmaps() in a more organized way.
The config_df is a data.frame with one row per coverage heatmap
to produce, and all options associated with that heatmap
are stored on the same row of the data.frame.
file: character file path to the coverage matrix file
name: character string used as a name, used in difference calculations
label: character string used as a label above each heatmap
display: logical indicating whether to display each heatmap
group: character string indicating a panel group, used to share
certain settings across groups of heatmap panels. When this value
is not defined, each heatmap is defined as its own group.
color: character string that refers to a specific color gradient,
or a comma-delimited series of colors to use as a color gradient.
See below for details.
ceiling: numeric used to define the maximum numeric value
applied to the color gradient, default=0.7
ylim: numeric used to define a fixed y-axis range used for the
profile plot atop each heatmap. When this value is absent or NA
the maximum y-axis value for the group is used.
control: character string that defines an optional control name
used to subtract coverage from this row.
Colors can be define one of a few ways:
name of a color gradient
name of a single color
comma-delimited colors, either as color names, or as hex colors
in the format #FFAABB.
Color gradients from RColorBrewer are recognized. You can view
linear color gradients: RColorBrewer::display.brewer.all(type="seq")
divergent color gradients: RColorBrewer::display.brewer.all(type="div")
Color gradients are also recognized from viridis, however these are
only linear: viridis::inferno(), viridis::magma(), viridis::plasma()
viridis::cividis(),viridis::viridis().
Other jam coverage heatmap functions:
coverage_matrix2nmat(),
get_nmat_ceiling(),
nmatlist2heatmaps(),
validate_heatmap_params(),
zoom_nmatlist(),
zoom_nmat()
Other jam coverage heatmap functions:
coverage_matrix2nmat(),
get_nmat_ceiling(),
nmatlist2heatmaps(),
validate_heatmap_params(),
zoom_nmatlist(),
zoom_nmat()