Plot a representative spontaneous current trace

plot_spontaneous_current_trace() generates a plot of raw current amplitude over time for a specified sweep from an ABF file. It requires a dataframe generated from raw .abf data with import_ABF_file(). The function returns a ggplot object with an optional scale bar.

Usage

plot_spontaneous_current_trace(
  data,
  plot_colour = "#000000",
  plot_category,
  plot_treatment,
  sex,
  state,
  letter,
  include_scale_bar = "yes",
  include_scale_bar_label = "yes",
  scale_bar_label_size = 4,
  trace_annotation = "",
  trace_annotation_x_position = 1,
  trace_annotation_y_position = 6,
  geom_text_family = "",
  geom_text_colour = "#000000",
  geom_text_size = 5,
  plot_episode = "epi1",
  trace_thickness = 0.8,
  scale_bar_x_start = 2.8,
  scale_bar_x_length = 0.2,
  scale_bar_y_length = 20,
  scale_bar_y_start = -30,
  scale_bar_linewidth = 0.75,
  scale_bar_label_y_nudge = 1.5,
  plot_x_min = 1,
  plot_x_max = 3,
  plot_y_min = -60,
  plot_y_max = 15,
  filename_suffix = "",
  save_plot_png = "no",
  ggplot_theme = patchclampplotteR_theme()
)

Arguments

data: A dataframe containing at least these columns: time, episode, current, voltage, time_sec. An easy way to obtain this is by importing a raw .abf file through the import_ABF_file() function.
plot_colour: A character value naming the colour of the plot.
plot_category: A numeric value specifying the category, which can be used to differentiate different protocol types. In the sample dataset for this package, plot_category == 2 represents experiments where insulin was applied continuously after a 5-minute baseline period.
plot_treatment: A character value specifying the treatment you would like to plot (e.g. "Control"). plot_treatment represents antagonists that were present on the brain slice, or the animals were fasted, etc.
sex: An optional character value ("male" or "female"), which will be added to the file name.
state: A character value describing if the recording was taken during the baseline period or post-treatment/protocol. Examples include "Baseline", "Post-insulin". The state will be included in the .png filename if save_plot_png = "yes".
letter: An optional character value describing the recording letter ID, (e.g. "A", "AB") that will be appended to the filename.
include_scale_bar: A character value that determines if a scale bar will be added to the plot. Allowed values are "yes" and "no".
include_scale_bar_label: A character value ("yes" or "no") describing whether to include text labels on the scale bar. If "yes", the text annotation values will be pulled from scale_bar_x_length and scale_bar_y_length.
scale_bar_label_size: A numeric value describing the size of the scale bar annotation text. Defaults to 4.
trace_annotation: A character value (e.g. "Baseline") that will be added as text on the plot. Useful for labelling traces for publications and presentations. Defaults to "Baseline".
trace_annotation_x_position: A numeric value for the location of the trace_annotation on the x-axis. Defaults to 1.
trace_annotation_y_position: A numeric value for the location of the trace_annotation on the y-axis. Defaults to 6.
geom_text_family: A character value describing the font family used for the scale bar annotations. Defaults to "" (empty, will use default system font), but can be replaced with a named font. Use a package like extrafont to load system fonts into R.
geom_text_colour: A character value describing the colour of the trace_annotation text. Defaults to "#000000".
geom_text_size: A numeric value describing the size of the trace_annotation text. Defaults to 5.
plot_episode: A character value describing the sweep (e.g. epi1) that will be used for the plot.
trace_thickness: A numeric value describing the thickness of the line.
scale_bar_x_start: A numeric value (in seconds) describing the x-axis position of the scale bar (default is 1.25).
scale_bar_x_length: A numeric value describing the horizontal span (in seconds) of the scale bar. This will automatically be converted and displayed in milliseconds (default is 0.5).
scale_bar_y_length: A numeric value describing the vertical span (in pA) of the scale bar (default is 20).
scale_bar_y_start: A numeric value describing the y-axis position (in pA) of the scale bar (default is 15).
scale_bar_linewidth: A numeric value describing the thickness of the scalebar line (default is 0.4).
scale_bar_label_y_nudge: An optional numeric value that will add additional padding between the scale bar x-axis label and the scale bar. Defaults to 1.5.
plot_x_min: A numeric value describing the minimum value on the x-axis (in seconds). Defaults to 1.
plot_x_max: A numeric value describing the maximum value on the x-axis (in seconds). Defaults to 3.
plot_y_min: A numeric value describing the minimum value on the y-axis (in pA). Defaults to -80. !!Warning!! Be sure to check your raw current amplitudes and adjust this to avoid cutting off data!!
plot_y_max: A numeric value describing the maximum value on the y-axis (in pA). Defaults to 5. !!Warning!! Be sure to check your raw current amplitudes and adjust this to avoid cutting off data!!
filename_suffix: Optional character value to add a suffix to the filename of the .png file created with this plot. Could be useful if you have specified a custom list of treatments.
save_plot_png: A character ("yes" or "no"). If "yes", the plot will be saved as a .png using ggsave(). The filepath depends on the current type, but they will all go in subfolders below Figures/ in your project directory.
ggplot_theme: The name of a ggplot theme or your custom theme. This will be added as a layer to a ggplot object. The default is patchclampplotteR_theme(), but other valid entries include theme_bw(), theme_classic() or the name of a custom ggplot theme stored as an object.

Value

A ggplot object. If save_plot_png is defined as "yes", it will also generate a .png file in the folder Figures/Spontaneous-currents/Representative-Traces relative to the project directory, with the plot_category, plot_treatment, and state included in the filename.

Examples

plot_spontaneous_current_trace(
  data = sample_abf_file,
  plot_colour = "#6600cc",
  plot_category = 2,
  plot_treatment = "Control",
  state = "Baseline",
  plot_episode = "epi1",
  trace_annotation = "Baseline",
  geom_text_colour = "#6600cc"
)

Usage

Arguments

Value

See also

Examples