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Set the panel width/height of a plot object to a fixed value.

Source: R/SCP-plot.R
panel_fix.Rd

The ggplot object, when stored, can only specify the height and width of the entire plot, not the panel. The latter is obviously more important to control the final result of a plot. This function can set the panel width/height of plot to a fixed value and rasterize it.

Usage

panel_fix(
  x = NULL,
  panel_index = NULL,
  respect = NULL,
  width = NULL,
  height = NULL,
  margin = 1,
  padding = 0,
  units = "in",
  raster = FALSE,
  dpi = 300,
  BPPARAM = BiocParallel::SerialParam(),
  return_grob = FALSE,
  bg_color = "white",
  save = NULL,
  verbose = FALSE,
  ...
)

panel_fix_overall(
  x,
  panel_index = NULL,
  respect = NULL,
  width = NULL,
  height = NULL,
  margin = 1,
  units = "in",
  raster = FALSE,
  dpi = 300,
  BPPARAM = BiocParallel::SerialParam(),
  return_grob = FALSE,
  bg_color = "white",
  save = NULL,
  verbose = TRUE
)

Arguments

x

A ggplot object, a grob object, or a combined plot made by patchwork or cowplot package.

panel_index

Specify the panel to be fixed. If NULL, will fix all panels.

respect

If a logical, this indicates whether row heights and column widths should respect each other.

width

The desired width of the fixed panels.

height

The desired height of the fixed panels.

margin

The margin to add around each panel, in inches. The default is 1 inch.

padding

The padding to add around each panel, in inches. The default is 0 inches.

units

The units in which height, width and margin are given. Can be mm, cm, in, etc. See unit.

raster

Whether to rasterize the panel.

dpi

Plot resolution.

BPPARAM

An BiocParallelParam instance determining the parallel back-end to be used during building the object made by patchwork package.

return_grob

If TRUE then return a grob object instead of a wrapped patchwork object.

bg_color

Plot background color.

save

NULL or the file name used to save the plot.

verbose

Whether to print messages.

...

Unused.

Examples

library(ggplot2)
p <- ggplot(data = mtcars, aes(x = mpg, y = wt, colour = cyl)) +
  geom_point() +
  facet_wrap(~gear, nrow = 2)
# fix the size of panel
panel_fix(p, width = 5, height = 3, units = "cm")

# rasterize the panel
panel_fix(p, width = 5, height = 3, units = "cm", raster = TRUE, dpi = 30)


# panel_fix will build and render the plot when the input is a ggplot object.
# so after panel_fix, the size of the object will be changed.
object.size(p)
#> 13984 bytes
object.size(panel_fix(p, width = 5, height = 3, units = "cm"))
#> 1398888 bytes

## save the plot with appropriate size
# p_fix <- panel_fix(p, width = 5, height = 3, units = "cm")
# plot_size <- attr(p_fix, "size")
# ggsave(
#   filename = "p_fix.png", plot = p_fix,
#   units = plot_size$units, width = plot_size$width, height = plot_size$height
# )
## or save the plot directly
# p_fix <- panel_fix(p, width = 5, height = 3, units = "cm", save = "p_fix.png")

# fix the panel of the plot combined by patchwork
data("pancreas_sub")
p1 <- CellDimPlot(pancreas_sub, "Phase", aspect.ratio = 1) # ggplot object
p2 <- FeatureDimPlot(pancreas_sub, "Ins1", aspect.ratio = 0.5) # ggplot object
p <- p1 / p2 # plot is combined by patchwork
# fix the panel size for each plot, the width will be calculated automatically based on aspect.ratio
panel_fix(p, height = 1)


# fix the panel of the plot combined by plot_grid
if (requireNamespace("cowplot", quietly = TRUE)) {
  p1 <- CellDimPlot(pancreas_sub, c("Phase", "SubCellType"), label = TRUE) # plot is combined by patchwork
  p2 <- FeatureDimPlot(pancreas_sub, c("Ins1", "Gcg"), label = TRUE) # plot is combined by patchwork
  p <- cowplot::plot_grid(p1, p2, nrow = 2) # plot is combined by plot_grid
  # fix the size of panel for each plot
  panel_fix(p, height = 1)
  # rasterize the panel while keeping all labels and text in vector format
  panel_fix(p, height = 1, raster = TRUE, dpi = 30)
}


# fix the panel of the heatmap
ht1 <- GroupHeatmap(pancreas_sub,
  features = c(
    "Sox9", "Anxa2", "Bicc1", # Ductal
    "Neurog3", "Hes6", # EPs
    "Fev", "Neurod1", # Pre-endocrine
    "Rbp4", "Pyy", # Endocrine
    "Ins1", "Gcg", "Sst", "Ghrl" # Beta, Alpha, Delta, Epsilon
  ),
  group.by = c("CellType", "SubCellType"),
  show_row_names = TRUE
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
# the size of the heatmap is not fixed and can be resized by zooming the viewport.
ht1$plot

# fix the size of the heatmap according the current viewport
panel_fix(ht1$plot)

# rasterize the heatmap body
panel_fix(ht1$plot, raster = TRUE, dpi = 30)

# fix the size of overall heatmap including annotation and legend
panel_fix(ht1$plot, height = 4, width = 6)


ht2 <- GroupHeatmap(pancreas_sub,
  features = pancreas_sub[["RNA"]]@var.features,
  group.by = "SubCellType",
  n_split = 5, nlabel = 20,
  db = "GO_BP", species = "Mus_musculus", anno_terms = TRUE,
  height = 4, width = 1 # Heatmap body size for two groups
)
#> 'magick' package is suggested to install to give better rasterization.
#> 
#> Set `ht_opt$message = FALSE` to turn off this message.
#> [2023-11-21 08:02:40.109273] Start Enrichment
#> Workers: 2
#> Species: Mus_musculus
#> Loading cached db: GO_BP version:3.17.0 nterm:16027 created:2023-11-21 07:14:20.545084
#> Convert ID types for the database: GO_BP
#> Connect to the Ensembl archives...
#> Using the 103 version of biomart...
#> Connecting to the biomart...
#> Searching the dataset mmusculus ...
#> Connecting to the dataset mmusculus_gene_ensembl ...
#> Converting the geneIDs...
#> Error in collect(., Inf): Failed to collect lazy table.
#> Caused by error in `db_collect()`:
#> ! Arguments in `...` must be used.
#> ✖ Problematic argument:
#> • ..1 = Inf
#> ℹ Did you misspell an argument name?
# the size of the heatmap is already fixed
ht2$plot
#> Error in eval(expr, envir, enclos): object 'ht2' not found
# when no height/width is specified, panel_fix does not change the size of the heatmap.
panel_fix(ht2$plot)
#> Error in eval(expr, envir, enclos): object 'ht2' not found
# rasterize the heatmap body
panel_fix(ht2$plot, raster = TRUE, dpi = 30)
#> Error in eval(expr, envir, enclos): object 'ht2' not found
# however, gene labels on the left and enrichment annotations on the right cannot be adjusted
panel_fix(ht2$plot, height = 5, width = 10)
#> Error in eval(expr, envir, enclos): object 'ht2' not found