nmathm_row_order: Make coverage heatmaps

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

Make coverage heatmaps

Description

(IN DEV) Make coverage heatmaps using a simple set of config options

Usage

nmathm_row_order(HM, ...)

Arguments

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.

Details

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

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().

Value

list of rownames, where each list represents one row_slice used in the heatmap, as defined by nmatlist2heatmaps() arguments partition or k_clusters.

See Also

Other jam coverage heatmap functions: coverage_matrix2nmat(), get_nmat_ceiling(), nmatlist2heatmaps(), recenter_nmatlist(), restrand_nmatlist(), validate_heatmap_params(), zoom_nmatlist(), zoom_nmat()

Other jam coverage heatmap functions: coverage_matrix2nmat(), get_nmat_ceiling(), nmatlist2heatmaps(), recenter_nmatlist(), restrand_nmatlist(), validate_heatmap_params(), zoom_nmatlist(), zoom_nmat()

Examples

# display RColorBrewer linear gradients
RColorBrewer::display.brewer.all(type="seq")

# display RColorBrewer divergent gradients
RColorBrewer::display.brewer.all(type="div")

# viridis linear gradients
jamba::showColors(list(
   inferno=viridis::inferno(11),
   magma=viridis::magma(11),
   plasma=viridis::plasma(11),
   cividis=viridis::cividis(11),
   viridis=viridis::viridis(11)))

# jam_linear
jamba::showColors(jam_linear)

# jam_divergent
jamba::showColors(jam_divergent)

Row order for nmatlist coverage heatmap

Row order for nmatlist coverage heatmap

This function is a simple wrapper function to return the
row order for the output of `nmatlist2heatmaps()`.
It traverses the `ComplexHeatmap::Heatmap` object,
including optional row slices when the rows are
partitioned. It returns the actual character
vector of rownames, optionally split into a `list`.

When the heatmap is fully drawn, for example with
`nmatlist2heatmaps(..., do_plot=TRUE)`, the output
object includes an element `"HM_drawn"` which also contains
the row order as displayed in that heatmap. Otherwise,
the output contains element `"draw"` with the heatmap
that would be drawn by `ComplexHeatmap::draw()`. In
this case the row order has not yet been defined,
however this function will evaluate the relevant
criteria to determine the row order that would be
rendered. And note that this process takes slightly
more time, but much less time than rendering the
entire set of heatmaps.

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