Plots result of signifPlot.

Usage

signifPlot(
  results,
  fdr = FALSE,
  type = "bubble",
  breaks = NULL,
  comparisonGroup = NULL,
  colours = c("#4575B4", "white", "#D73027"),
  marksToPlot = NULL,
  cutoff = 0.05
)

Arguments

results: Data frame obtained from spicy.
fdr: TRUE if FDR correction is used.
type: Where to make a bubble plot or heatmap.
breaks: Vector of 3 numbers giving breaks used in pheatmap. The first number is the minimum, the second is the maximum, the third is the number of breaks.
comparisonGroup: A string specifying the name of the outcome group to compare with the base group.
colours: Vector of colours to use in pheatmap.
marksToPlot: Vector of marks to include in pheatmap.
cutoff: significance threshold for circles in bubble plot.

Value

a pheatmap object

Examples

data(spicyTest)

p <- signifPlot(spicyTest, breaks = c(-3, 3, 0.5))
#> Scanning ttf files in /usr/share/fonts/, /usr/local/share/fonts/ ...
#> Extracting .afm files from .ttf files...
#> /usr/share/fonts/truetype/dejavu/DejaVuSans-Bold.ttf
#>  : DejaVuSans-Bold already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf
#>  : DejaVuSans-BoldOblique already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSans-ExtraLight.ttf
#>  : DejaVuSans-ExtraLight already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf
#>  : DejaVuSans-Oblique already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSans.ttf
#>  : DejaVuSans already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansCondensed-Bold.ttf
#>  : DejaVuSansCondensed-Bold already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansCondensed-BoldOblique.ttf
#>  : DejaVuSansCondensed-BoldOblique already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansCondensed-Oblique.ttf
#>  : DejaVuSansCondensed-Oblique already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansCondensed.ttf
#>  : DejaVuSansCondensed already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansMono-Bold.ttf
#>  : DejaVuSansMono-Bold already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansMono-BoldOblique.ttf
#>  : DejaVuSansMono-BoldOblique already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansMono-Oblique.ttf
#>  : DejaVuSansMono-Oblique already registered in fonts database. Skipping.
#> /usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf
#>  : DejaVuSansMono already registered in fonts database. Skipping.
#> Found FontName for 0 fonts.
#> Scanning afm files in /home/runner/work/_temp/Library/extrafontdb/metrics
# plot includes unicode characters, do not use default pdf device
ggplot2::ggsave(p, filename = tempfile(), device = cairo_pdf)
#> Saving 6.67 x 6.67 in image