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Create a ridgeline plot

Source: R/plot_ridge.R
ridgePlot.Rd

Plot continuous numeric features as a series of density ridges. Particularly useful for making comparisons between feature distributions within a population.

Usage

ridgePlot(
  gobject,
  feats,
  ...,
  group_by = NULL,
  group_by_subset = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  stat = "density_ridges",
  ridge_alpha = 1,
  ridge_scale = 5,
  scale_axis = "identity",
  axis_offset = NULL,
  background_color = "white",
  remove_na = NULL,
  show_legend = FALSE,
  title = NULL,
  theme_param = list(),
  cow_n_col = NULL,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "ridgePlot",
  verbose = NULL
)

Arguments

gobject

giotto object

feats

features to plot. Passed to GiottoClass::spatValues()

...

additional params to pass to GiottoClass::spatValues()

group_by

character. Create multiple plots based on cell annotation column

group_by_subset

character. subset the group_by factor column

spat_unit

spatial unit (e.g. "cell")

feat_type

feature type (e.g. "rna", "dna", "protein")

stat

character. A stat accepted by ggridges::geom_density_ridges()

ridge_alpha

numeric. Alpha to use for ridgeline plot. Value from 0 to 1.

ridge_scale

numeric. Controls height of ridges.

scale_axis

character (default = "log2". An x axis scaling to use. This value is passed to ggplot2::scale_x_continuous(). Set "identity" to remove scaling.

axis_offset

numeric. Value to add to values. When this value is not provided and axis_scale is one of "log", "log2", or "log10", a axis_offset of 1 is used by default.

background_color

background color

remove_na

logical. If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show_legend

logical. Whether to show legend

title

character. Title for plot

theme_param

list of additional params passed to ggplot2::theme()

cow_n_col

cowplot param: how many columns

cow_rel_h

cowplot param: relative heights of rows (e.g. c(1,2))

cow_rel_w

cowplot param: relative widths of columns (e.g. c(1,2))

cow_align

cowplot param: how to align

show_plot

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

save_param

list of saving parameters, see showSaveParameters

default_save_name

default save name for saving, don't change, change save_name in save_param

verbose

be verbose

Value

ggplot

Examples

g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.12

# plot normalized expresion of first 6 features
ridgePlot(g,
    feats = head(rownames(g)),
    expression_values = "normalized",
    scale_axis = "log2"
)
#> Error: package 'ggridges' is not yet installed
#> 
#>  To install:
#> install.packages(c("ggridges"))

# plot distribution on PCA PCs
ridgePlot(g,
    feats = sprintf("Dim.%d", 1:20),
    scale_axis = "identity"
)
#> Error: package 'ggridges' is not yet installed
#> 
#>  To install:
#> install.packages(c("ggridges"))

ridgePlot(g,
    feats = sprintf("Dim.%d", 1:20),
    scale_axis = "identity",
    group_by = "leiden_clus",
    group_by_subset = c(1:4)
)
#> Error: package 'ggridges' is not yet installed
#> 
#>  To install:
#> install.packages(c("ggridges"))