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Venndir class

Source: R/Venndir-class.R
Venndir-class.Rd

Venndir class

Details

This object is intended to contain all the required data to produce a venndir figure. The components in this object can be edited.

Slots:

  • jps: JamPolygon containing the set and overlap polygons.

    • Columns "x","y" contain polygon coordinates, see JamPolygon-class for details on multi-part polygons, and polygons with holes.

    • The polygon type is defined with column type and values "set" or "overlap".

    • The "set" polygons are intended to be the full circle for each set, but may be NA or NULL to indicate the set is empty.

    • The "overlap" polygons are expected to be contained inside "set" polygons, and each overlap polygon may be multi-polygons with or without holes. For example, the "set" polygon for set_A which is a circle fully contained inside another set set_B. The "overlap" polygon for set_A would be empty, since there is no region unique to set_A. However the "overlap" polygon set_A&set_B would contain the full circle defined by "set" polygon set_A. Lastly the "overlap" polygon for set_B would be a circle with a hole located at "overlap" set_A&set_B. or ellipse. The overlap polygons are polygons, possibly multi-part with or without holes, or may be NA or NULL to indicate that this overlap does not have a corresponding polygon.

    • The name column contains set or overlap names, where multiple sets are concatenated with "&" by default. or ellipse corresponding to each set in setlist), and the overlap polygons. Where an overlap does not exist, the polygon coordinates will be empty, or will have entirely NA values for "x" and "y".

  • label_df: data.frame which contains information about Venn labels placement and content. It should contain one row for each Venn overlap. When data contains signed overlaps, each overlap is sub-divided by the combination of overlap signs, with one row per overlap and overlap signs. Overlap signs are summarized based upon argument overlap_type, see signed_overlaps().

    • "overlap_sign" represents the combination of overlap name, and the overlap sign across all sets.

    • "text" indicates the count label to be displayed.

    • "venn_counts" indicates the numeric number of Venn overlaps in each row.

    • "item" should be a list that contains character vectors of items in each overlap set. Column "item" is optional.

    • "nsets" indicates the number of sets involved in the overlap.

    • "x", "y" represent the label coordinate to use inside each polygon overlap. When the label is displayed outside the polygon, the values "x_offset" and "y_offset" are added to "x" and "y", respectively. In this way, a line segment can be drawn from the outer label back to the corresponding polygon.

    • "color" indicates the color for each label. Note the actual color may be modified based upon the background fill color to maximize the contrast and visibility of the color. For example blue on a dark background is displayed as light blue.

    • "fontsize" indicates the base font size, prior to any optional adjustment with font_cex.

    • "fill" indicates an optional color fill behind the count label. When NULL (default) there is no color fill. This value is usually populated by argument label_style which is passed to venndir_label_preset().

    • "border" indicates an optional border around count labels, and is handled similar to "fill".

    • "padding", "padding_unit", "r", and "r_unit" are used with gridtext::richtext_grob() to define padding around count labels, and optional rounded corners when border is displayed.

    • Other columns are intended for internal use by render_venndir() and are not yet fully editable.

  • setlist: list with the setlist used to create the Venn overlaps. Previously this data could be inferred from label_df which was tedious, and required column "item" which is optional. That said, setlist can be an empty list().

  • metadata: list with optional metadata, intended for future expansion, such as plot title.

See also

Other venndir advanced: curate_venn_labels(), get_venndir_curate_df(), modify_venndir_overlap(), nudge_venndir_label()

Examples

v <- venndir(make_venn_test(100, 2, do_signed=TRUE), do_plot=FALSE)
# default print for Venndir gives a concise summary
v
#> class: Venndir
#> number of sets: 2
#> number of polygons: 2 sets, 3 overlaps
#> overlap_type: 'concordance'
#> sets:
#>   set_name setlist_labels legend_labels set_colors size
#> 1    set_A          set_A         set_A    #EEC12E   32
#> 2    set_B          set_B         set_B    #D54848   16

# example with overlap which is not shown
overlaps <- c(set_A=187, set_B=146, set_C=499,
   `set_A&set_B`=1,
   `set_A&set_C`=181,
   `set_B&set_C`=219,
   `set_A&set_B&set_C`=20);
setlist_o <- counts2setlist(overlaps)
v3 <- venndir(setlist_o, proportional=TRUE, do_plot=FALSE)
# the print includes '1 overlap cannot be displayed'
v3
#> class: Venndir
#> number of sets: 3
#> number of polygons: 3 sets, 7 overlaps
#> overlap_type: 'overlap'
#> 1 overlap cannot be displayed:
#> * `set_A&set_B`=1
#> sets:
#>   set_name setlist_labels legend_labels set_colors size
#> 1    set_A          set_A         set_A    #EEC12E  389
#> 2    set_B          set_B         set_B    #D54848  386
#> 3    set_C          set_C         set_C    #9F8DFF  919

# the warnings(v3) also contain the overlaps not displayed
warnings(v3)
#> Warning message:
#> In "set_A&set_B" : 1

# the overlap names can be extracted directly
as.character(warnings(v3))
#> [1] "set_A&set_B"

# the counts for each overlap are also available
as.numeric(names(warnings(v3)))
#> [1] 1