Prune and summarize raw current data per minute

make_pruned_eEPSC_df() creates a dataframe of evoked or spontaneous current data summarized per minute (or some other user-defined interval). Current amplitudes are collapsed down into the mean amplitude per minute. This is equivalent to GraphPad Prism's "prune rows" function to reduce data to summary values for every n rows.

Usage

make_pruned_EPSC_data(
  data = patchclampplotteR::sample_raw_eEPSC_df,
  current_type = "eEPSC",
  min_time_value = 0,
  max_time_value = 25,
  baseline_length = 5,
  interval_length = 1,
  decimal_places = 2,
  save_output_as_RDS = "no"
)

Arguments

data: A data.frame object generated using make_normalized_EPSC_data(). It must contain the columns outlined in the Required columns section below, which will already be generated for you from the output of make_normalized_EPSC_data().
current_type: A character describing the current type. Allowed values are "eEPSC" or "sEPSC".
min_time_value: Minimum time value (numeric; in minutes), which defaults to 0.
max_time_value: Maximum recording length (numeric; in minutes). All data points will be filtered to time values less than or equal to this value. Defaults to 25.
baseline_length: Length of the baseline (numeric; in minutes). Refers to data collected before applying a hormone, antagonist, or a protocol like high frequency stimulation. Defaults to 5.
interval_length: Length of each interval (in minutes). Used to divide the dataset into broad ranges for statistical analysis. Defaults to 1 for one summary point per minute.
decimal_places: A numeric value indicating the number of decimal places the data should be rounded to. Used to reduce file size and prevent an incorrect representation of the number of significant digits.
save_output_as_RDS: A character ("yes" or "no") describing if the resulting object should be saved as an RDS file in the raw data folder.

Value

A list containing 3 dataframes that can be viewed and used for further analyses in R. These dataframes are:

individual_cells
for_table
all_cells

I highly recommend assigning the list to an object named something like pruned_eEPSC_df to make it easy to reference the dataframes with logical names (e.g. pruned_eEPSC_df$all_cells). The dataframes are:

individual_cells A dataframe containing current data for each individual cell, but the data are reduced to a summary point per per minute (or another value if a different interval_length is set). This dataframe contains columns already in the raw data, like category, letter and sex plus new columns.

New columns for evoked current data (current_type == "eEPSC") include:
- interval_pruned A character value describing the interval that was used for the pruning function. If the data are pruned per minute, this will be "t0to1", "t1to2", "t2to3", etc.
- mean_P1 The mean amplitude (in pA) of the first evoked current (P1) during a specific interval. This is an average of all data points within each interval. For example, the mean_P1 for the interval "t0to1" contains the average current amplitude of all data points within the first minute of the recording.
- sd_P1 The standard deviation of P1.
- n The number of data points used.
- se The standard error of P1.
- cv The coefficient of variation of P1.
- cv_inverse_square The inverse coefficient of variation, which is then squared. This is to enable variance analysis, as in Huijstee & Kessels (2020).
- baseline_mean The mean amplitude of the first evoked current during the baseline period.
- category, letter, sex, treatment, etc. Columns which are from the raw data. For a definition of these columns, please see the documentation for make_normalized_EPSC_data().
- time The upper time value of the interval (e.g. 2 minutes for "t1to2") which is used on the x-axis of plots such as in plot_raw_current_data().
New columns for spontaneous current data (current_type == "sEPSC") include:
- mean_amplitude The mean amplitude of the normalized spontaneous current amplitude for a specific interval (obtained from make_normalized_EPSC_data()).
- mean_raw_amplitude The mean amplitude of the raw spontaneous current amplitude for a specific interval.
- sd_amplitude The standard deviation of the normalized spontaneous current amplitudes.
- n The number of currents
- frequency The frequency (in Hz) of currents during the interval.
- se The standard error of the normalized spontaneous current amplitudes.
- letter, category, interval, synapses Columns inherited from the raw data.
- time The upper time value of the interval (e.g. 2 minutes for "t1to2") which is used on the x-axis of plots such as in plot_summary_current_data().
- baseline_range A logical value required for the baseline transformation. It is set to TRUE when time is within the baseline period (e.g. Time <= 5) and FALSE at all other times.
- baseline_mean_frequency The mean spontaneous frequency during the baseline period.
- frequency_transformed The spontaneous current frequency (in Hz), normalized relative to the baseline current frequency.
for_table A dataframe containing two columns: letter and P1_transformed (for eEPSC) or spont_amplitude_transformed (for sEPSC). The current data is collapsed into a single row for each letter, with the current data for each letter stored as a list. This is required to create sparklines of current amplitude over time within the cell summary table. See make_cell_summary_df() and make_interactive_summary_table().
all_cells A dataframe consisting of all data within a single treatment grouped and summarized per minute (or some other variable if you change interval_length to be something other than 1). Columns like category and sex are retained from the raw data.

New columns for evoked current data (current_type == "eEPSC") are:
- interval_pruned A character value describing the interval that was used for the pruning function. If the data are pruned per minute, this will be "t0to1", "t1to2", "t2to3", etc.
- mean_P1_all_cells The mean amplitude (in pA) of the first evoked current (P1) during a specific interval across all cells.
- sd_P1_all_cells The standard deviation of P1.
- n The number of data points used.
- se_P1_all_cells The standard error of P1.
- cv_P1_all_cells The coefficient of variation of P1.
New columns for spontaneous current data (current_type == "sEPSC") are:
- interval_pruned A character value describing the interval that was used for the pruning function. If the data are pruned per minute, this will be "t0to1", "t1to2", "t2to3", etc.
- mean_all_amplitude The mean normalized amplitude (in % Baseline) of the spontaneous current amplitudes during a specific interval across all cells.
- mean_all_raw_amplitude The mean raw amplitude (in pA) of the spontaneous current amplitudes during a specific interval across all cells.
- sd_all_amplitude The standard deviation of the normalized spontaneous current amplitudes across all cells.
- n The number of data points used.
- se_all_amplitude The standard error of the normalized spontaneous currents across all cells.
- sd_all_raw_amplitude The standard deviation of the raw spontaneous current amplitudes across all cells.
- se_raw_amplitude The standard error of the raw spontaneous currents across all cells.
- mean_all_frequency The mean normalized frequency (% Baseline frequency) of all spontaneous current amplitudes across all cells during the interval.
- sd_all_frequency The standard deviation of the normalized frequency of all spontaneous current amplitudes across all cells during the interval.
- se_frequency The standard error of the normalized frequency of all spontaneous current amplitudes across all cells during the interval.
- mean_all_raw_frequency The mean raw frequency (Hz) of all spontaneous current amplitudes across all cells during the interval.
- sd_all_raw_frequency The standard deviation of the raw frequency of all spontaneous current amplitudes across all cells during the interval.
- se_raw_frequency The standard error of the raw frequency of all spontaneous current amplitudes across all cells during the interval.

Required evoked currents columns

These columns will all be generated automatically in make_normalized_EPSC_data(), but for more details, you can look at sample_raw_eEPSC_df to see an example of what the incoming raw dataset in the data argument should look like. If the data are evoked currents (current_type == "eEPSC"), the data must contain the basic columns mentioned in Required basic columns plus these columns:

PPR A numeric value that represents the paired pulse ratio (PPR) of the evoked currents, generated in make_normalized_EPSC_data().
interval A character value indicating the interval that the data belong to (e.g. "t0to5" for the first 5 minutes, "t5to10"). Generated automatically in make_normalized_EPSC_data().
baseline_range A logical value required for the baseline transformation. It is set to TRUE when time is within the baseline period (e.g. time <= 5) and FALSE at all other times. Generated automatically in make_normalized_EPSC_data().
baseline_mean A numeric value representing the mean evoked current amplitude during the baseline period. There is a different baseline_mean for each letter. Generated automatically in make_normalized_EPSC_data().
P1_transformed A numeric value representing the first evoked current amplitude (pA) normalized relative to the mean amplitude during the recording's baseline. Generated automatically in make_normalized_EPSC_data().
P2_transformed A numeric value representing the second evoked current amplitude (pA) normalized relative to the mean amplitude during the recording's baseline. Generated automatically in make_normalized_EPSC_data().

Required spontaneous currents columns

If the data are spontaneous currents (current_type == "sEPSC"), the data must contain the basic columns mentioned in Required basic columns plus the columns listed below. For more detail, have a look at sample_raw_sEPSC_df to see an example of what the incoming raw dataset in the data argument should look like.

interval A character value indicating the interval that the data belong to (e.g. "t0to5" for the first 5 minutes, "t5to10"). Generated automatically in make_normalized_EPSC_data().
baseline_range A logical value required for the baseline transformation. It is set to TRUE when time is within the baseline period (e.g. Time <= 5) and FALSE at all other times. Generated automatically in make_normalized_EPSC_data().
baseline_mean A numeric value representing the mean evoked current amplitude during the baseline period. There is a different baseline_mean for each letter. Generated automatically in make_normalized_EPSC_data().
amplitude_transformed A numeric value representing the spontaneous current amplitude (pA) normalized relative to the mean amplitude during the recording's baseline. Generated automatically in make_normalized_EPSC_data().

Required basic columns

It doesn't matter if the data are evoked or current type - these columns should be included in your data.

letter A character value that is a unique identifier for a single recording. Used to link data sets for evoked or spontaneous currents and cell-characteristics.
synapses A character value (e.g. "Glutamate" or "GABA").
sex A character value (e.g. "Male" or "Female").
treatment A character value (e.g. "Control", "HNMPA").
time A numeric value that represents time in minutes. This column is autogenerated in add_new_cells().
ID A character value for the recording filename.
X A numeric value representing the x-value of the cell's location in µm. Leave this blank if you don't have this data.
Y A numeric value representing the y-value of the cell's location in µm. Leave this blank if you don't have this data.
age A numeric value representing the animal's age. Can be any value as long as the time units are consistent throughout (e.g. don't mix up days and months when reporting animal ages).
animal A numeric value representing the animal's ID or number.
category A numeric value representing the experiment type. Used to assign top-level groups for further analyses, with treatment as subgroups.
cell A character or numeric value representing the cell. For example, use 3.1.1 for animal #3, slice #1, cell #1.

Evoked current data:

If the data are evoked currents (current_type == "eEPSC"), the data must contain the basic columns mentioned in Required basic columns plus these columns:

P1 A numeric value representing the amplitude of the first evoked current in pA.
P2 A numeric value representing the amplitude of the second evoked current in pA.

Spontaneous current data:

If the data are spontaneous currents (current_type == "sEPSC"), the data must contain the basic columns mentioned in Required basic columns plus these columns:

recording_num A numeric value representing the recording number. This was incorporated before we switched to concatenating all recordings into one, but it needs to remain here to prevent breaking previous projects. It should be set to 1.
trace A numeric value representing the trace (automatically generated in Clampfit) where the current occurred.
time_of_peak A numeric value representing the time of the peak in milliseconds relative to trace number. This is automatically calculated in Clampfit.
time A numeric value representing the absolute time when the current happened, relative to the start of the recording. This is autogenerated. See add_new_cells() for a description of how the true time value (time) is calculated from the recording_num and trace.
amplitude A numeric value representing the amplitude of the evoked current in pA.

Examples

make_pruned_EPSC_data(
  data = sample_raw_eEPSC_df,
  current_type = "eEPSC",
  min_time_value = 0,
  max_time_value = 25,
  baseline_length = 5,
  interval_length = 1,
  decimal_places = 2
)
#> $individual_cells
#> # A tibble: 473 × 14
#>    category letter sex   treatment interval_pruned mean_P1 sd_P1     n    se
#>    <fct>    <fct>  <fct> <fct>     <fct>             <dbl> <dbl> <dbl> <dbl>
#>  1 2        AO     Male  Control   t0to1             36.4  13.8     13  3.83
#>  2 2        AO     Male  Control   t1to2             38.1  21.4     12  6.18
#>  3 2        AO     Male  Control   t2to3             39.4  22.2     12  6.41
#>  4 2        AO     Male  Control   t3to4             39.2  18.5     12  5.34
#>  5 2        AO     Male  Control   t4to5             30.8  19.7     12  5.69
#>  6 2        AO     Male  Control   t5to6             21.3  15.6     12  4.52
#>  7 2        AO     Male  Control   t6to7             13.6  17.4     12  5.01
#>  8 2        AO     Male  Control   t7to8             14.4  16.5     12  4.77
#>  9 2        AO     Male  Control   t8to9              5.68  2       12  0.58
#> 10 2        AO     Male  Control   t9to10             7.45  5.84    12  1.69
#> # ℹ 463 more rows
#> # ℹ 5 more variables: cv <dbl>, cv_inverse_square <dbl>, time <dbl>,
#> #   baseline_mean <dbl>, synapses <fct>
#> 
#> $for_table
#> # A tibble: 19 × 2
#>    letter P1_transformed
#>    <fct>  <list>        
#>  1 AO     <dbl [25]>    
#>  2 AZ     <dbl [25]>    
#>  3 BN     <dbl [25]>    
#>  4 BO     <dbl [25]>    
#>  5 BT     <dbl [25]>    
#>  6 CG     <dbl [25]>    
#>  7 CZ     <dbl [25]>    
#>  8 FT     <dbl [25]>    
#>  9 FX     <dbl [25]>    
#> 10 GF     <dbl [25]>    
#> 11 GI     <dbl [25]>    
#> 12 GK     <dbl [25]>    
#> 13 GR     <dbl [25]>    
#> 14 GX     <dbl [25]>    
#> 15 HB     <dbl [25]>    
#> 16 HC     <dbl [25]>    
#> 17 HG     <dbl [23]>    
#> 18 HN     <dbl [25]>    
#> 19 L      <dbl [25]>    
#> 
#> $all_cells
#> # A tibble: 198 × 10
#>    category interval_pruned sex    treatment   mean_P1_all_cells sd_P1_all_cells
#>    <fct>    <fct>           <fct>  <fct>                   <dbl>           <dbl>
#>  1 2        t0to1           Female Control                 141.            NA   
#>  2 2        t0to1           Female HNMPA                   117.            11.0 
#>  3 2        t0to1           Female PPP                      97.3           10.2 
#>  4 2        t0to1           Female PPP_and_HN…              94.2           NA   
#>  5 2        t0to1           Male   Control                  95.9           11.2 
#>  6 2        t0to1           Male   HNMPA                   123.            21.5 
#>  7 2        t0to1           Male   PPP                     110.            13.6 
#>  8 2        t0to1           Male   PPP_and_HN…             116.             4.9 
#>  9 2        t1to2           Female Control                 104.            NA   
#> 10 2        t1to2           Female HNMPA                    96.0            1.74
#> # ℹ 188 more rows
#> # ℹ 4 more variables: n <dbl>, se_P1_all_cells <dbl>, cv_P1_all_cells <dbl>,
#> #   time <dbl>
#> 

make_pruned_EPSC_data(
  data = sample_raw_sEPSC_df,
  current_type = "sEPSC",
  min_time_value = 0,
  max_time_value = 25,
  baseline_length = 5,
  interval_length = 1,
  decimal_places = 2
)
#> $individual_cells
#> # A tibble: 195 × 17
#> # Groups:   letter [7]
#>    category letter sex    treatment interval_pruned mean_amplitude
#>    <fct>    <fct>  <fct>  <fct>     <fct>                    <dbl>
#>  1 2        AZ     Female Control   t0to1                    104. 
#>  2 2        AZ     Female Control   t1to2                     98.9
#>  3 2        AZ     Female Control   t2to3                     97.7
#>  4 2        AZ     Female Control   t3to4                    101. 
#>  5 2        AZ     Female Control   t4to5                     98.7
#>  6 2        AZ     Female Control   t4to5                     98.7
#>  7 2        AZ     Female Control   t5to6                     95.4
#>  8 2        AZ     Female Control   t6to7                     96.9
#>  9 2        AZ     Female Control   t7to8                     97.6
#> 10 2        AZ     Female Control   t8to9                     94.5
#> # ℹ 185 more rows
#> # ℹ 11 more variables: mean_raw_amplitude <dbl>, sd_amplitude <dbl>, n <dbl>,
#> #   frequency <dbl>, se <dbl>, interval <fct>, synapses <fct>, time <dbl>,
#> #   baseline_range <lgl>, baseline_mean_frequency <dbl>,
#> #   frequency_transformed <dbl>
#> 
#> $for_table
#> # A tibble: 7 × 2
#>   letter spont_amplitude_transformed
#>   <fct>  <list>                     
#> 1 AZ     <dbl [29]>                 
#> 2 BO     <dbl [26]>                 
#> 3 FX     <dbl [28]>                 
#> 4 GR     <dbl [26]>                 
#> 5 GX     <dbl [29]>                 
#> 6 HC     <dbl [28]>                 
#> 7 L      <dbl [29]>                 
#> 
#> $all_cells
#> # A tibble: 167 × 19
#>    category interval_pruned sex    treatment     mean_all_amplitude
#>    <fct>    <fct>           <fct>  <fct>                      <dbl>
#>  1 2        t0to1           Female Control                    104. 
#>  2 2        t0to1           Female PPP                         98.5
#>  3 2        t0to1           Male   Control                     82.3
#>  4 2        t0to1           Male   HNMPA                       98.1
#>  5 2        t0to1           Male   PPP                        106. 
#>  6 2        t0to1           Male   PPP_and_HNMPA              105. 
#>  7 2        t1to2           Female Control                     98.9
#>  8 2        t1to2           Female PPP                        101. 
#>  9 2        t1to2           Male   Control                     97.6
#> 10 2        t1to2           Male   HNMPA                      101. 
#> # ℹ 157 more rows
#> # ℹ 14 more variables: mean_all_raw_amplitude <dbl>, sd_all_amplitude <dbl>,
#> #   n <dbl>, se_amplitude <dbl>, sd_all_raw_amplitude <dbl>,
#> #   se_raw_amplitude <dbl>, mean_all_frequency <dbl>, sd_all_frequency <dbl>,
#> #   se_frequency <dbl>, mean_all_raw_frequency <dbl>,
#> #   sd_all_raw_frequency <dbl>, se_raw_frequency <dbl>, time <dbl>,
#> #   interval <fct>
#>