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Line Plot

Source: R/lineplot.R
LinePlot.Rd

Visualizing the change of a numeric value over the progression of a categorical variable.

Usage

LinePlot(
  data,
  x,
  y = NULL,
  group_by = NULL,
  group_by_sep = "_",
  split_by = NULL,
  split_by_sep = "_",
  fill_point_by_x_if_no_group = TRUE,
  color_line_by_x_if_no_group = TRUE,
  add_bg = FALSE,
  bg_palette = "stripe",
  bg_palcolor = NULL,
  bg_alpha = 0.2,
  add_errorbars = FALSE,
  errorbar_width = 0.1,
  errorbar_alpha = 1,
  errorbar_color = "grey30",
  errorbar_linewidth = 0.75,
  errorbar_min = NULL,
  errorbar_max = NULL,
  errorbar_sd = NULL,
  highlight = NULL,
  highlight_size = pt_size - 0.75,
  highlight_color = "red2",
  highlight_alpha = 0.8,
  pt_alpha = 1,
  pt_size = 5,
  keep_na = FALSE,
  keep_empty = FALSE,
  line_type = "solid",
  line_width = 1,
  line_alpha = 0.8,
  add_hline = FALSE,
  hline_type = "solid",
  hline_width = 0.5,
  hline_color = "black",
  hline_alpha = 1,
  theme = "theme_this",
  theme_args = list(),
  palette = "Paired",
  palcolor = NULL,
  x_text_angle = 0,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  facet_by = NULL,
  facet_scales = "fixed",
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_byrow = TRUE,
  facet_args = list(),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)

Arguments

data

A data frame.

x

A character string specifying the column name of the data frame to plot for the x-axis.

y

A character string specifying the column name of the data frame to plot for the y-axis.

group_by

Columns to group the data for plotting For those plotting functions that do not support multiple groups, They will be concatenated into one column, using group_by_sep as the separator

group_by_sep

A character string specifying the separator to use when concatenating multiple columns.

split_by

The column(s) to split data by and plot separately.

split_by_sep

The separator for multiple split_by columns. See split_by

fill_point_by_x_if_no_group

A logical value indicating whether to color the points by the x-axis values when there is no group_by column.

color_line_by_x_if_no_group

A logical value indicating whether to color the lines by the x-axis values

add_bg

A logical value indicating whether to add a background to the plot.

bg_palette

The palette to use for the background.

bg_palcolor

The color to use for the background.

bg_alpha

The alpha value of the background.

add_errorbars

A logical value indicating whether to add error bars to the plot.

errorbar_width

The width of the error bars.

errorbar_alpha

The alpha value of the error bars.

errorbar_color

The color to use for the error bars. If "line", the error bars will be colored the same as the lines.

errorbar_linewidth

The line width of the error bars.

errorbar_min

The column in the data frame containing the lower bound of the error bars.

errorbar_max

The column in the data frame containing the upper bound of the error bars.

errorbar_sd

The column in the data frame containing the standard deviation of the error bars. If errorbar_min and errorbar_max are not provided, this column will be used to calculate the error bars. errorbar_min = y - errorbar_sd, errorbar_max = y + errorbar_sd. If errorbar_min and errorbar_max are provided, this column will be ignored.

highlight

A vector of indexes or rownames to select the points to highlight. It could also be an expression (in string) to filter the data.

highlight_size

The size of the highlighted points.

highlight_color

A character vector specifying the color of the highlighted points. Default is "red".

highlight_alpha

A numeric value specifying the transparency of the highlighted points. Default is 1.

pt_alpha

The alpha value of the points.

pt_size

The size of the points.

keep_na

A logical value or a character to replace the NA values in the data. It can also take a named list to specify different behavior for different columns. If TRUE or NA, NA values will be replaced with NA. If FALSE, NA values will be removed from the data before plotting. If a character string is provided, NA values will be replaced with the provided string. If a named vector/list is provided, the names should be the column names to apply the behavior to, and the values should be one of TRUE, FALSE, or a character string. Without a named vector/list, the behavior applies to categorical/character columns used on the plot, for example, the x, group_by, fill_by, etc.

keep_empty

One of FALSE, TRUE and "level". It can also take a named list to specify different behavior for different columns. Without a named list, the behavior applies to the categorical/character columns used on the plot, for example, the x, group_by, fill_by, etc.

  • FALSE (default): Drop empty factor levels from the data before plotting.

  • TRUE: Keep empty factor levels and show them as a separate category in the plot.

  • "level": Keep empty factor levels, but do not show them in the plot. But they will be assigned colors from the palette to maintain consistency across multiple plots. Alias: levels

line_type

The type of line to draw.

line_width

The width of the line.

line_alpha

The alpha value of the line.

add_hline

A numeric value indicating the y-intercept of a horizontal line to add to the plot. If FALSE, no horizontal line will be added.

hline_type

The type of line to draw for the horizontal line.

hline_width

The width of the horizontal line.

hline_color

The color of the horizontal line. When group_by is provided, this can be TRUE to use the same color as the lines.

hline_alpha

The alpha value of the horizontal line.

theme

A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".

theme_args

A list of arguments to pass to the theme function.

palette

A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different split_by values.

palcolor

A character string specifying the color to use in the palette. A named list can be used to specify the colors for different split_by values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).

x_text_angle

A numeric value specifying the angle of the x-axis text.

aspect.ratio

A numeric value specifying the aspect ratio of the plot.

legend.position

A character string specifying the position of the legend. if waiver(), for single groups, the legend will be "none", otherwise "right".

legend.direction

A character string specifying the direction of the legend.

facet_by

A character string specifying the column name of the data frame to facet the plot. Otherwise, the data will be split by split_by and generate multiple plots and combine them into one using patchwork::wrap_plots

facet_scales

Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See ggplot2::facet_wrap

combine

Whether to combine the plots into one when facet is FALSE. Default is TRUE.

nrow

A numeric value specifying the number of rows in the facet.

ncol

A numeric value specifying the number of columns in the facet.

byrow

A logical value indicating whether to fill the plots by row.

facet_nrow

A numeric value specifying the number of rows in the facet. When facet_by is a single column and facet_wrap is used.

facet_ncol

A numeric value specifying the number of columns in the facet. When facet_by is a single column and facet_wrap is used.

facet_byrow

A logical value indicating whether to fill the plots by row. Default is TRUE.

facet_args

A list of arguments to pass to ggplot2::facet_wrap() or ggplot2::facet_grid(). when there is no group_by column.

title

A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.

subtitle

A character string specifying the subtitle of the plot.

xlab

A character string specifying the x-axis label.

ylab

A character string specifying the y-axis label.

seed

The random seed to use. Default is 8525.

axes

A string specifying how axes should be treated. Passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. Options are:

  • 'keep' will retain all axes in individual plots.

  • 'collect' will remove duplicated axes when placed in the same run of rows or columns of the layout.

  • 'collect_x' and 'collect_y' will remove duplicated x-axes in the columns or duplicated y-axes in the rows respectively.

axis_titles

A string specifying how axis titltes should be treated. Passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. Options are:

  • 'keep' will retain all axis titles in individual plots.

  • 'collect' will remove duplicated titles in one direction and merge titles in the opposite direction.

  • 'collect_x' and 'collect_y' control this for x-axis titles and y-axis titles respectively.

guides

A string specifying how guides should be treated in the layout. Passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. Options are:

  • 'collect' will collect guides below to the given nesting level, removing duplicates.

  • 'keep' will stop collection at this level and let guides be placed alongside their plot.

  • 'auto' will allow guides to be collected if a upper level tries, but place them alongside the plot if not.

design

Specification of the location of areas in the layout, passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. When specified, nrow, ncol, and byrow are ignored. See patchwork::wrap_plots() for more details.

...

Additional arguments.

Value

A ggplot object or wrap_plots object or a list of ggplot objects

Examples

# \donttest{
data <- data.frame(
   x = factor(c("A", "B", "C", "D", "A", "B", "C", "D"), levels = LETTERS[1:6]),
   y = c(10, 8, 16, 4, 6, 12, 14, 2),
   group = c("G1", "G1", "G1", "G1", "G2", "G2", "G2", "G2"),
   facet = c("F1", "F1", "F2", "F2", "F3", "F3", "F4", "F4")
)

LinePlot(data, x = "x", y = "y")

LinePlot(data, x = "x", y = "y", highlight = "group == 'G1'",
   fill_point_by_x_if_no_group = FALSE, color_line_by_x_if_no_group = FALSE)

LinePlot(data, x = "x", y = "y", group_by = "group")

LinePlot(data, x = "x", y = "y", group_by = "group",
   add_hline = 10, hline_color = "red")

LinePlot(data, x = "x", y = "y", group_by = "group", add_bg = TRUE,
   highlight = "y > 10")

LinePlot(data, x = "x", y = "y", group_by = "group", facet_by = "facet")

LinePlot(data, x = "x", y = "y", group_by = "group", split_by = "facet")

LinePlot(data, x = "x", y = "y", split_by = "group",
         palcolor = list(G1 = c("red", "blue"), G2 = c("green", "black")))


# keep_na and keep_empty
data <- data.frame(
   x = factor(c("A", "B", NA, "D", "A", "B", NA, "D"), levels = LETTERS[1:4]),
   y = c(10, 8, 16, 4, 6, 12, 14, 2),
   group = factor(c("G1", "G1", "G1", NA, NA, "G3", "G3", "G3"),
     levels = c("G1", "G2", "G3")),
   facet = c("F1", "F1", "F2", "F2", "F3", "F3", "F4", "F4")
)

LinePlot(data, x = "x", y = "y", keep_na = TRUE)

LinePlot(data, x = "x", y = "y", keep_empty = TRUE)

LinePlot(data, x = "x", y = "y", keep_empty = 'level')

LinePlot(data, x = "x", y = "y", group_by = "group", keep_na = TRUE)

LinePlot(data, x = "x", y = "y", group_by = "group", keep_empty = TRUE)

LinePlot(data, x = "x", y = "y", group_by = "group",
   keep_empty = list(x = TRUE, group = 'level'))

# }