Plot cell location data — plot_cell_coordinates

This function enables you to plot your cell locations on a coordinate system with an image of a brain slice in the background. The points are coloured by the percent change in evoked or spontaneous current amplitude over time.

Usage

plot_cell_coordinates_data(
  data,
  background_slice_filename,
  background_slice_height = 800,
  background_slice_width = 800,
  plot_category,
  include_all_treatments = "yes",
  list_of_treatments = NULL,
  scale_bar_x_start = 700,
  scale_bar_x_length = 100,
  scale_bar_y_start = 100,
  scale_bar_y_length = 100,
  scale_bar_units = "um",
  include_scale_bar_label = "yes",
  scale_bar_thickness = 0.8,
  scale_bar_colour = "white",
  scale_bar_label_size = 4,
  geom_point_size = 3,
  geom_text_family = "",
  geom_point_alpha = 0.95,
  legend_width = 0.4,
  legend_title = "Change in eEPSC\namplitude (%)",
  legend_text_size = 6,
  legend_title_size = 12,
  legend_title_bottom_margin = 10,
  legend_height = 10,
  filename_suffix,
  save_plot_png = "no",
  theme_options,
  ggplot_theme = NULL,
  ...
)

Arguments

data: A dataframe generated from make_summary_EPSC_data(). If current_type = "eEPSC", this must be the percent change dataframe generated from make_summary_EPSC_data(). Use $percent_change to access this dataframe. If current_type = "sEPSC", this can either be $percent_change_amplitude or $percent_change_frequency.
background_slice_filename: A character value describing the location of the background slice image. This may be a png or a jpeg. It must contain just the background slice, and the height and width must be known values in scale_bar_units.
background_slice_height: The height of the background slice image in scale_bar_units. Defaults to 800.
background_slice_width: The width of the background slice image in scale_bar_units. Defaults to 800.
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.
include_all_treatments: A character ("yes" or "no") specifying if the plot will include data from all treatments. If "no", you must specify a list of treatments in list_of_treatments.
list_of_treatments: A list of character values describing the treatments that will be in the plot. Defaults to NULL, since include_all_treatments is "yes" by default.
scale_bar_x_start: The starting location of the scale bar on the x-axis in scale_bar_units. Defaults to 700.
scale_bar_x_length: The length of the scale bar on the x-axis in scale_bar_units.
scale_bar_y_start: The starting location of the scale bar on the y-axis in scale_bar_units. Defaults to 100.
scale_bar_y_length: The length of the scale bar on the y-axis in scale_bar_units.
scale_bar_units: The units of the scale bar. Often, it will be "um".
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_thickness: A numeric value describing the thickness of the scale bar. Defaults to 0.8.
scale_bar_colour: A character value (named colour of hex value) describing the colour of the scale bar. Defaults to "black".
scale_bar_label_size: A numeric value describing the size of the scale bar annotation text. Defaults to 4.
geom_point_size: A numeric value describing the size of the points. Defaults to 3.
geom_text_family: A character value describing the font family used for the scale bar annotations. Defaults to "", but can be replaced with a named font. Use a package like extrafont to load system fonts into R.
geom_point_alpha: A numeric value describing the transparency of the points. Defaults to 0.95, but can be reduced to better view the brain slice below.
legend_width: The width of the legend colourbar. Defaults to 0.4.
legend_title: A character value for the colourbar title. Defaults to "Change in eEPSC amplitude (%)"
legend_text_size: The size of the text labels used in the legend. Defaults to 6.
legend_title_size: A numeric value for the size of the colourbar legend title. Defaults to 12.
legend_title_bottom_margin: A numeric value for the bottom margin of the colourbar legend title. Defaults to 10.
legend_height: The height of the legend colourbar. Defaults to 10.
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.
theme_options: A dataframe containing theme options, defaults to sample_theme_options. See sample_theme_options for an example of what this dataframe should look like and how you can customize these values.
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.
...: Additional arguments passed to ggplot2::scale_color_viridis_c() such as begin, end, option and direction.

Value

A ggplot object. If save_plot_png == "yes", it will also generate a .png file in Figures/Cell-coordinates-plot. The .png filename will contain the plot_category.

Examples


plot_cell_coordinates_data(
  data = sample_summary_eEPSC_df$percent_change_data,
  background_slice_filename = import_ext_data("DMH-brain-slice.jpg"),
  plot_category = 2,
  option = "plasma",
  theme_options = sample_theme_options
)