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Save line plots with errorbars by group

Source: R/effect_plots.R
save_group_lineplots.Rd

Plots the change in the feature abundances as a function of e.g. time. A line is drawn for each group and error bars are added. A separate plot is drawn for each feature.

Usage

save_group_lineplots(
  object,
  all_features = FALSE,
  save = TRUE,
  file_path = NULL,
  format = "emf",
  x,
  group,
  title = "Feature_ID",
  subtitle = NULL,
  fun.data = "mean_cl_boot",
  fun = NULL,
  fun.min = NULL,
  fun.max = NULL,
  position_dodge_amount = 0.2,
  color_scale = getOption("notame.color_scale_dis"),
  text_base_size = 14,
  line_width = 0.5,
  point_size = 4,
  title_line_length = 40,
  theme = theme_bw(base_size = text_base_size),
  assay.type = NULL,
  ...
)

Arguments

object

a SummarizedExperiment or MetaboSet object

all_features

logical, should all features be used? If FALSE (the default), flagged features are removed before visualization

save

logical, if false, the plots are not saved but returned as a list

file_path

character, a file path for PDF or prefix added to the file paths for other formats

format

character, format in which the plots should be saved

x

character, name of the column to be used as x-axis

group

character, name of the column containing group information, used for coloring

title, subtitle

column names from feature data to use as plot title/filename and subtitle. Set to NULL for no title/subtitle, this creates running numbered filenames

fun.data

passed to stat_summary and used for errorbars, "A function that is given the complete data and should return a data frame with variables ymin, y, and ymax."

fun.min, fun, fun.max

Alternative to fun.data, passed to stat_summary, "supply three individual functions that are each passed a vector of x's and should return a single number"

position_dodge_amount

numeric: how much the group mean points should dodge away from each other

color_scale

the color scale as returned by a ggplot function

text_base_size

integer, base size for text in figures

line_width

numeric, width of the lines

point_size

numeric, size of the points

title_line_length

integer, maximum length of the title line in characters, passed to str_wrap

theme

a ggplot theme to be added to the plot

assay.type

character, assay to be used in case of multiple assays

...

other arguments to graphic device functions, like width and height

Value

By default, the function is invoked for its plot-saving side effect. The function returns a list of plots when save = FALSE.

See also

save_plot, stat_summary

Examples

data(example_set)
save_group_lineplots(drop_qcs(example_set)[1:10],
  file_path = "./group_line_plots.pdf",
  format = "pdf", x = "Time", group = "Group"
)
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:24] Saved line plots with mean line to: ./group_line_plots.pdf
save_group_lineplots(drop_qcs(example_set)[1:10],
  file_path = "./group_line_plots/",
  format = "png", x = "Time", group = "Group"
)
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:24] Saved to: ./group_line_plots/HILIC_neg_259_9623a4_4322.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:24] Saved to: ./group_line_plots/HILIC_neg_108_1065a2_6121.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:25] Saved to: ./group_line_plots/HILIC_neg_158_23a1_4128.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:25] Saved to: ./group_line_plots/HILIC_neg_251_0056a0_6161.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:25] Saved to: ./group_line_plots/HILIC_neg_401_52a4_211.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:25] Saved to: ./group_line_plots/HILIC_neg_400_7045a5_3842.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:25] Saved to: ./group_line_plots/HILIC_neg_304_014a7_1311.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:25] Saved to: ./group_line_plots/HILIC_neg_276_6328a2_7734.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:26] Saved to: ./group_line_plots/HILIC_neg_118_9111a4_1865.png
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> INFO [2025-06-23 22:38:26] Saved to: ./group_line_plots/HILIC_neg_446_9413a2_315.png
#> INFO [2025-06-23 22:38:26] Saved line plots with mean line to: ./group_line_plots/
# Plot one feature
save_group_lineplots(drop_qcs(example_set[1, ]), save = FALSE, x = "Time",
  group = "Group")
#> Just a remainder, creating a long list of plots takes a lot of memory!
#> [[1]]
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.
#> Warning: Computation failed in `stat_summary()`.
#> Caused by error in `fun.data()`:
#> ! The package "Hmisc" is required.

#>