Apply Cnet border color by directionality

Usage

apply_cnet_direction(
  cnet,
  hitim = NULL,
  col = circlize::colorRamp2(breaks = c(-1, 0, 1), colors = c("blue", "grey80",
    "firebrick3")),
  col_l_max = 80,
  hide_solo_pie = TRUE,
  frame_blank = default_igraph_values()$vertex$frame.color,
  frame_lwd_blank = 0.2,
  border_lwd = 2,
  do_reorder = FALSE,
  verbose = FALSE,
  ...
)

Arguments

cnet

igraph object with node attribute "pie.color" populated as a list of character vectors, named by enrichment. The enrichment names should match colnames(hitim).

hitim

numeric matrix with values centered at zero for no change, positive values +1 for up-regulation, and negative values -1 for down-regulation. The values are converted to color using color function col.

col

function that takes numeric input and assigns a color. The default assigns red for positive values, blue for negative values, and white for zero, using colorjam::col_div_xf(1.2).

col_l_max

numeric maximum HCL Lightness, default 80, for output colors. For example, the middle color in "RdBu_r" is nearly white, the col_l_max can be used to apply a darker grey.

hide_solo_pie

logical default TRUE, whether a single-color border for a multi-part pie node should only apply the color to the overall node with 'frame.color', and not apply the color to each pie wedge using 'pie.border'.

Default hide_solo_pie=TRUE: when all wedges (one or more) have the same pie.border color, the 'pie.border' is defined as NA, and 'frame.color' is assigned to this color. The effect is to display the outline color and not each wedge. Both 'pie.lwd' and 'frame.lwd' will be assigned border_lwd, and since 'pie.border' is NA it will not be rendered. Only the 'frame.color' will be rendered.
When hide_solo_pie=FALSE each pie wedge border color is assigned to 'pie.border', frame.color will be assigned 'frame_blank', and 'frame.lwd' will be assigned 'frame_lwd_blank' which is useful for displaying a small outer frame for each node.

frame_blank

character string to define the color used for 'frame.color' when colors are defined in 'pie.border'. The default uses the igraph defaults, currently 'black'. In this case, the frame is drawn around the inner pie.border colors, and only serves to add visual clarity. The frame border can be blank frame_blank="transparent" or can be a thinner line, controlled with frame_lwd_blank=0.2.

frame_lwd_blank

numeric line width, default 0.2, for nodes that have "blank" frame, which also means the 'pie.border' colors must also defined. In this case the frame border can be invisible (frame_lwd_blank=0) or a very thin line (default frame_lwd_blank=0.2) to surround the inner borders drawn with 'pie.border'.

border_lwd

numeric line width, default 2, used when a node matches rownames(hitim). When the colors are applied to 'pie.color', the border is defined with 'pie.lwd'. When colors are applied to 'frame.color', the border is defined with 'frame.lwd'.

do_reorder

logical default FALSE, whether to reorder nodes by node attributes such as color and border, by calling reorder_igraph_nodes(). When do_reorder=TRUE, other relevant arguments are passed through ... to reorder_igraph_nodes() in particular:

colorV: to control the expected order of colors. It should be supplied if known upfront.
sortAttributes: to customize the default attribute sort order.
nodeSortBy: to customize the x-/y- axis arrangement.
orderByAspect: to enable x-/y- sorting by the aspect ratio of nodes in the group. For example, tall-skinny node groups should sort by y-axis first, short-wide node groups should sort by x-axis first.

...

additional arguments are passed to reorder_igraph_nodes() when do_reorder=TRUE.

Details

This function specifically requires the "pie.color" node attribute of the cnet object igraph is populated with a list of colors whose name is the enrichment, and matches colnames(hitim) of the supplied hit incidence matrix.

The node names V(cnet)$name also must match rownames(hitim), otherwise the "pie.border" and "coloredrect.border" is assigned its previous value. In that case "frame.color" retains its original value.

This function may be run multiple times with different hitim, for example using geneIMdirection and enrichIMdirection in two steps.

When there are multiple colors for a given node, they are populated in node attributes "pie.border" in list form. For these nodes, the attribute "frame.color" is set to NULL so it is not displayed on top of the pie wedge colors.

When there are no matching rownames(hitim), or all colors are identical, the "pie.border" is populated with NULL, so the pie wedges do not each show a color. Also for single-wedge pie nodes, this process avoids drawing a small line at the top of each node. Instead the attribute "frame.color" is populated with the one unique border color, so that only the outer border is colorized.

Todo

Consider permitting input to be a simple igraph, then creating pie.color, pie.border, pie.border.lwd attributes even if they previously did not exist. It would probably optionally also use colorV to colorize each component of multi-component nodes.

Apply Cnet border color by directionality

Usage

Arguments

Details

Todo

See also