Title: Exploratory Data Analysis using Tiled One-Dimensional Graphics
Version: 0.1.0
Description: Streamlines exploratory data analysis by providing a turnkey approach to visualising n-dimensional data which graphically reveals correlative or associative relationships between 2 or more features. Represents all dataset features as distinct, vertically aligned bar or tile plots, with plot types auto-selected based on whether variables are categorical or numeric.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
URL: https://github.com/selkamand/gg1d, https://selkamand.github.io/gg1d/
BugReports: https://github.com/selkamand/gg1d/issues
Imports: assertions (≥ 0.2.0), cli, ggiraph, ggplot2, ggtext, patchwork (≥ 1.3.0), rank (≥ 0.1.1), rlang
Suggests: covr, knitr, rmarkdown, testthat (≥ 3.0.0)
Config/testthat/edition: 3
Depends: R (≥ 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2024-12-07 01:39:11 UTC; selkamand
Author: Sam El-Kamand ORCID iD [aut, cre], Children's Cancer Institute Australia [cph]
Maintainer: Sam El-Kamand <sam.elkamand@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-09 19:40:02 UTC

Make strings prettier for printing

Description

Takes an input string and 'beautify' by converting underscores to spaces and

Usage

beautify(string, autodetect_units = TRUE)

Arguments

string

input string

autodetect_units

automatically detect units (e.g. mm, kg, etc) and wrap in brackets.

Value

string

Parse a tibble and ensure it meets standards

Description

Parse a tibble and ensure it meets standards

Usage

column_info_table(
  data,
  maxlevels = 6,
  col_id = NULL,
  cols_to_plot,
  tooltip_column_suffix = "_tooltip",
  ignore_column_regex = "_ignore$",
  palettes,
  colours_default,
  colours_default_logical,
  verbose
)

Arguments

data

data.frame to autoplot (data.frame)

maxlevels

for categorical variables, what is the maximum number of distinct values to allow (too many will make it hard to find a palette that suits). (number)

col_id

name of column to use as an identifier. If null, artificial IDs will be created based on row-number.

cols_to_plot

names of columns in data that should be plotted. By default plots all valid columns (character)

tooltip_column_suffix

the suffix added to a column name that indicates column should be used as a tooltip (string)

ignore_column_regex

a regex string that, if matches a column name, will cause that column to be exclude from plotting (string) (default: "_ignore$")

palettes

A list of named vectors. List names correspond to data column names (categorical only). Vector names to levels of columns. Vector values are colours, the vector names are used to map values in data to a colour.

colours_default

Default colors for categorical variables without a custom palette.

colours_default_logical

Colors for binary variables: a vector of three colors representing TRUE, FALSE, and NA respectively (character).

verbose

Numeric value indicating the verbosity level:

  • 2: Highly verbose, all messages.

  • 1: Key messages only.

  • 0: Silent, no messages.

Value

tibble with the following columns:

  1. colnames

  2. coltype (categorical/numeric/tooltip/invalid)

  3. ndistinct (number of distinct values)

  4. plottable (should this column be plotted)

  5. tooltip_col (the name of the column to use as the tooltip) or NA if no obvious tooltip column found

AutoPlot an entire data.frame

Description

Visualize all columns in a data frame with gg1d's vertically aligned plots and automatic plot selection based on variable type. Plots are fully interactive, and custom tooltips can be added.

Usage

gg1d(
  data,
  col_id = NULL,
  col_sort = NULL,
  order_matches_sort = TRUE,
  maxlevels = 6,
  verbose = 2,
  drop_unused_id_levels = FALSE,
  interactive = TRUE,
  return = c("plot", "column_info", "data"),
  palettes = NULL,
  sort_type = c("frequency", "alphabetical"),
  desc = TRUE,
  limit_plots = TRUE,
  max_plottable_cols = 15,
  cols_to_plot = NULL,
  tooltip_column_suffix = "_tooltip",
  ignore_column_regex = "_ignore$",
  convert_binary_numeric_to_factor = TRUE,
  options = gg1d_options(show_legend = !interactive)
)

Arguments

data

data.frame to autoplot (data.frame)

col_id

name of column to use as an identifier. If null, artificial IDs will be created based on row-number.

col_sort

name of columns to sort on. To do a hierarchical sort, supply a vector of column names in the order they should be sorted (character).

order_matches_sort

should the column plots be stacked top-to-bottom in the order they appear in col_sort (flag)

maxlevels

for categorical variables, what is the maximum number of distinct values to allow (too many will make it hard to find a palette that suits). (number)

verbose

Numeric value indicating the verbosity level:

  • 2: Highly verbose, all messages.

  • 1: Key messages only.

  • 0: Silent, no messages.

drop_unused_id_levels

if col_id is a factor with unused levels, should these be dropped or included in visualisation

interactive

produce interactive ggiraph visualiastion (flag)

return

a string describing what this function should return. Options include:

  • plot: Return the gg1d visualisation (default)

  • colum_info: Return a data.frame describing the columns the dataset.

  • data: Return the processed dataset used for plotting.

palettes

A list of named vectors. List names correspond to data column names (categorical only). Vector names to levels of columns. Vector values are colours, the vector names are used to map values in data to a colour.

sort_type

controls how categorical variables are sorted. Numerical variables are always sorted in numerical order irrespective of the value given here. Options are alphabetical or frequency

desc

sort in descending order (flag)

limit_plots

throw an error when there are > max_plottable_cols in dataset (flag)

max_plottable_cols

maximum number of columns that can be plotted (default: 15) (number)

cols_to_plot

names of columns in data that should be plotted. By default plots all valid columns (character)

tooltip_column_suffix

the suffix added to a column name that indicates column should be used as a tooltip (string)

ignore_column_regex

a regex string that, if matches a column name, will cause that column to be exclude from plotting (string) (default: "_ignore$")

convert_binary_numeric_to_factor

If a numeric column conatins only values 0, 1, & NA, then automatically convert to a factor.

options

a list of additional visual parameters created by calling gg1d_options(). See gg1d_options for details.

Value

ggiraph interactive visualisation

Examples

path_gg1d <- system.file("example.csv", package = "gg1d")
df <- read.csv(path_gg1d, header = TRUE, na.strings = "")

# Create Basic Plot
gg1d(df, col_id = "ID", col_sort = "Glasses")

# Configure plot gg1d_options()
gg1d(
  lazy_birdwatcher,
  col_sort = "Magpies",
  palettes = list(
    Birdwatcher = c(Robert = "#E69F00", Catherine = "#999999"),
    Day = c(Weekday = "#999999", Weekend = "#009E73")
  ),
  options = gg1d_options(
    show_legend = TRUE,
    fontsize_barplot_y_numbers = 12,
    legend_text_size = 16,
    legend_key_size = 1,
    legend_nrow = 1,
  )
)

Visual Parameters for gg1d Plots

Description

Configures aesthetic and layout settings for plots generated by gg1d.

Usage

gg1d_options(
  colours_default = c("#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F",
    "#E5C494"),
  colours_default_logical = c(`TRUE` = "#648fff", `FALSE` = "#dc267f"),
  colours_missing = "grey90",
  show_legend_titles = FALSE,
  legend_title_position = c("top", "bottom", "left", "right"),
  legend_nrow = 4,
  legend_ncol = NULL,
  legend_title_size = NULL,
  legend_text_size = NULL,
  legend_key_size = 0.3,
  legend_orientation_heatmap = c("horizontal", "vertical"),
  show_legend = TRUE,
  legend_position = c("right", "left", "bottom", "top"),
  na_marker = "!",
  na_marker_size = 8,
  na_marker_colour = "black",
  show_na_marker_categorical = FALSE,
  show_na_marker_heatmap = FALSE,
  colours_heatmap_low = "purple",
  colours_heatmap_high = "seagreen",
  transform_heatmap = c("identity", "log10", "log2"),
  fontsize_values_heatmap = 3,
  show_values_heatmap = FALSE,
  colours_values_heatmap = "white",
  vertical_spacing = 0,
  numeric_plot_type = c("bar", "heatmap"),
  y_axis_position = c("left", "right"),
  width = 0.9,
  relative_height_numeric = 4,
  cli_header = "Running gg1d",
  interactive_svg_width = NULL,
  interactive_svg_height = NULL,
  fontsize_barplot_y_numbers = 8,
  max_digits_barplot_y_numbers = 3,
  fontsize_y_title = 12,
  beautify_text = TRUE
)

Arguments

colours_default

Default colors for categorical variables without a custom palette.

colours_default_logical

Colors for binary variables: a vector of three colors representing TRUE, FALSE, and NA respectively (character).

colours_missing

Color for missing (NA) values in categorical plots (string).

show_legend_titles

Display titles for legends (flag).

legend_title_position

Position of the legend title ("top", "bottom", "left", "right").

legend_nrow

Number of rows in the legend (number).

legend_ncol

Number of columns in the legend. If set, legend_nrow should be NULL (number).

legend_title_size

Size of the legend title text (number).

legend_text_size

Size of the text within the legend (number).

legend_key_size

Size of the legend key symbols (number).

legend_orientation_heatmap

should legend orientation be "horizontal" or "vertical".

show_legend

Display the legend on the plot (flag).

legend_position

Position of the legend ("right", "left", "bottom", "top").

na_marker

Text used to mark NA values in numeric plots (string).

na_marker_size

Size of the text marker for NA values (number).

na_marker_colour

Color of the NA text marker (string).

show_na_marker_categorical

Show a marker for NA values on categorical tiles (flag).

show_na_marker_heatmap

Show a marker for NA values on heatmap tiles (flag).

colours_heatmap_low

Color for the lowest value in heatmaps (string).

colours_heatmap_high

Color for the highest value in heatmaps (string).

transform_heatmap

Transformation to apply before visualizing heatmap values ("identity", "log10", "log2").

fontsize_values_heatmap

Font size for heatmap values (number).

show_values_heatmap

Display numerical values on heatmap tiles (flag).

colours_values_heatmap

Color for heatmap values (string).

vertical_spacing

Space between each data row in points (number).

numeric_plot_type

Type of visualization for numeric data: "bar" or "heatmap".

y_axis_position

Position of the y-axis ("left" or "right").

width

controls how much space is present between bars and tiles within each plot. Can be 0-1 where values of 1 makes bars/tiles take up 100% of available space (no gaps between bars).

relative_height_numeric

how many times taller should numeric plots be relative to categorical tile plots. Only taken into account if numeric_plot_type == "bar" (number)

cli_header

Text used for h1 header. Included so it can be tweaked by packages that use gg1d, so they can customise how the info messages appear.

interactive_svg_width, interactive_svg_height

width and height of the interactive graphic region (in inches). Only used when interactive = TRUE.

fontsize_barplot_y_numbers

fontsize of the text describing numeric barplot max & min values (number).

max_digits_barplot_y_numbers

Number of digits to round the numeric barplot max and min values to (number).

fontsize_y_title

fontsize of the y axis titles (a.k.a the data.frame column names) (number).

beautify_text

Beautify y-axis text and legend titles by capitalizing words and adding spaces (flag).

Value

A list of visualization parameters for gg1d.

Examples

path_gg1d <- system.file("example.csv", package = "gg1d")
df <- read.csv(path_gg1d, header = TRUE, na.strings = "")

# Create Basic Plot
gg1d(df, col_id = "ID", col_sort = "Glasses")

# Configure plot gg1d_options()
gg1d(
  lazy_birdwatcher,
  col_sort = "Magpies",
  palettes = list(
    Birdwatcher = c(Robert = "#E69F00", Catherine = "#999999"),
    Day = c(Weekday = "#999999", Weekend = "#009E73")
  ),
  options = gg1d_options(
    show_legend = TRUE,
    fontsize_barplot_y_numbers = 12,
    legend_text_size = 16,
    legend_key_size = 1,
    legend_nrow = 1,
  )
)

Lazy Birdwatcher Dataset

Description

A simulated dataset describing the number of magpies observed by two birdwatchers.

Usage

lazy_birdwatcher

Format

lazy_birdwatcher

A data frame with 45 rows and 3 columns:

Magpies

Number of magpies observed

Day

Was the day of observation a weekday or a weekend?

Birdwatcher

Name of the birdwatcher

GGplot breaks

Description

Find sensible values to add 2 breaks at for a ggplot2 axis

Usage

sensible_2_breaks(vector)

Arguments

vector

vector fed into ggplot axis you want to define sensible breaks for

Value

vector of length 2. first element descripts upper break position, lower describes lower break