This function creates a scatterplot of parameters such as raw amplitude grouped according to treatment. The data are limited to values from the baseline period, allowing for a quick comparison of baseline parameters across treatments. For evoked currents, only raw amplitude is available for comparison. For spontaneous currents, raw amplitude and raw frequency during the baseline period can be plotted.
Usage
plot_baseline_data(
data,
current_type = "eEPSC",
parameter = "raw_amplitude",
include_all_treatments = "yes",
list_of_treatments = NULL,
baseline_interval = "t0to5",
filename_suffix = "",
large_axis_text = "no",
plot_width = 8,
treatment_colour_theme,
theme_options,
save_plot_png = "no"
)Arguments
- data
A dataframe containing the summary data generated from
make_summary_EPSC_data().- current_type
A character describing the current type. Allowed values are "eEPSC" or "sEPSC".
- parameter
A character describing the parameter used on the y-axis. If
current_type == "eEPSC", the allowed parameter is "raw_amplitude". Ifcurrent_type == "sEPSC", the allowed parameters are "raw_amplitude" or "raw_frequency". Note: It does not make sense to use normalized/baseline transformed amplitudes, since these will all be 100, and the graph will be a flat line.- 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.
- baseline_interval
A character value indicating the name of the interval used as the baseline. Defaults to "t0to5", but can be changed. Make sure that this matches the baseline interval that you set in
make_normalized_EPSC_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.
- large_axis_text
A character ("yes" or "no"). If "yes", a ggplot theme layer will be applied which increases the axis text.
- plot_width
A numeric value specifying the width of the plot. Defaults to 8, but you will need to adjust this depending on how many treatments you have.
- treatment_colour_theme
A dataframe containing treatment names and their associated colours as hex values. See sample_treatment_names_and_colours for an example of what this dataframe should look like.
- theme_options
A dataframe containing theme options. See sample_theme_options for an example of what this dataframe should look like.
- 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.
Value
A ggplot object. If save_plot_png == "yes", it will also generate
a .png file in Figures/Evoked-currents/Output-summary-plots or
Figures/Spontaneous-currents/Output-summary-plots. The .png filename will
contain the parameter.
Examples
plot_baseline_data(
data = sample_summary_eEPSC_df,
current_type = "eEPSC",
parameter = "raw_amplitude",
include_all_treatments = "yes",
list_of_treatments = NULL,
baseline_interval = "t0to5",
large_axis_text = "no",
plot_width = 8,
treatment_colour_theme = sample_treatment_names_and_colours,
theme_options = sample_theme_options,
save_plot_png = "no"
)
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
