fill_panel

fill_panel

A convenience function adding graphical objects to a gtable constructed by multi_panel_figure.

Usage

fill_panel(
  figure,
  panel,
  row = "auto",
  column = "auto",
  label = NULL,
  label_just = c("right", "bottom"),
  panel_clip = c("on", "off", "inherit"),
  scaling = c("none", "stretch", "fit", "shrink"),
  allow_panel_overwriting = FALSE,
  verbose = TRUE,
  ...
)

Details

Currently supported as panel-representing objects (panel) are

1. ComplexHeatmap Heatmap or HeatmapList objects.

2. ggplot2 ggplot objects.

3. grid grob, gList, and gTree objects.

4. lattice trellis.objects.

5. Single character objects representing URLs or paths to image formats accessible by ImageMagick as used through magick, which will be read and placed into panels as requested.

Native resolution is determined from attributes in the file. If the attributes are not present, then the DPI is determined by the the multipanelfigure.defaultdpi global option, or 300 if this has not been set.

lattice-generated trellis.objects are converted to grobs using grid.grabExpr(print(x)), as are Heatmap and HeatmapLists from ComplexHeatmap - the side effects of which with respect to plot formatting are not well studied.

If the row argument is "auto", then the first row with a free panel is used. If the column argument is "auto", then the first column in the row with a free panel is used.

References

Graumann, J., and Cotton, R.J. (2018). multipanelfigure: Simple Assembly of Multiple Plots and Images into a Compound Figure. Journal of Statistical Software 84. doi: 10.18637/jss.v084.c03

See Also

gtable, multi_panel_figure

Aliases

• fill_panel
• addPanel
• addpanel
• add_panel

Examples

# NOT RUN {
 # Not testing - slow grid graphics makes CRAN timing excessive
# Create the figure layout
(figure <- multi_panel_figure(
  width = c(30,40,60),
  height = c(40,60,60,60),
  panel_label_type = "upper-roman"))

# Fill the top-left panel using a grob object directly
a_grob <- grid::linesGrob(arrow = grid::arrow())
figure %<>% fill_panel(a_grob)

# Add a ggplot object directly to the top row, second column.
# The panels are chosen automatically, but you can achieve the same effect
# using column = 2
a_ggplot <- ggplot2::ggplot(mtcars, ggplot2::aes(disp, mpg)) +
  ggplot2::geom_point()
figure %<>% fill_panel(a_ggplot)

# Bitmap images are added by passing the path to their file.
image_files <- system.file("extdata", package = "multipanelfigure") %>%
  dir(full.names = TRUE) %>%
  setNames(basename(.))

# Add the JPEG to the top row, third column
figure %<>% fill_panel(image_files["rhino.jpg"], column = 3)

# Add the PNG to the second and third row, first and second column
figure %<>% fill_panel(
  image_files["Rlogo.png"],
  row = 2:3, column = 1:2)

# Add the TIFF to the second row, third column
figure %<>% fill_panel(
  image_files["unicorn.svg"],
  row = 2, column = 3)

# lattice/trellis plot objects are also added directly
Depth <- lattice::equal.count(quakes$depth, number=4, overlap=0.1)
a_lattice_plot <- lattice::xyplot(lat ~ long | Depth, data = quakes)
# Add the lattice plot to the third row, third column
figure %<>% fill_panel(
  a_lattice_plot,
  row = 3, column = 3)

# Incorporate a gList object (such as produced by VennDigram)
if(requireNamespace("VennDiagram"))
{
  a_venn_plot <- VennDiagram::draw.pairwise.venn(50, 30, 20, ind = FALSE)
  # Add the Venn diagram to the fourth row, firstd column
  figure %<>% fill_panel(
    a_venn_plot,
    row = 4, column = 1)
}

# Incorporate a base plot figure
a_base_plot <- capture_base_plot(
 heatmap(
   cor(USJudgeRatings), Rowv = FALSE, symm = TRUE, col = topo.colors(16),
   distfun = function(c) as.dist(1 - c), keep.dendro = TRUE,
   cexRow = 0.5, cexCol = 0.5))
# Add the heatmap to the fourth row, second column
figure %<>% fill_panel(
  a_base_plot,
  row = 4, column = 2)

# Incorporate a ComplexHeatmap figure
require(ComplexHeatmap)
mat = matrix(rnorm(80, 2), 8, 10)
mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
rownames(mat) = letters[1:12]
colnames(mat) = letters[1:10]
ht = Heatmap(mat)
a_complex_heatmap <- ht + ht + ht
# Add the ComplexHeatmap to the fourth row, third column
(figure %<>% fill_panel(
  a_complex_heatmap,
  row = 4, column = 3))
# }