Count Phosphosites Based on Probability Threshold — get_count

This function processes a data frame to count unique phosphosites based on a specified probability threshold. It groups the data by a "Group" extracted from the `Sample` column, calculates the average phosphosite count for each group, and can optionally generate a bar plot to visualize the results.

Usage

get_count_phosphosite(data, prob_threshold, plot = c("bar_plot", "no"))

Arguments

data: A data frame containing the data. It must have columns named `Sample`, `phosphosites`, and `Probability`. The `Sample` column is expected to be in the format 'sampleID_groupName' (e.g., 'p1_control', 'p3_dose-1').
prob_threshold: A numeric value between 0 and 1. This is the probability cutoff; the function will only consider phosphosites with a `Probability` value greater than or equal to this threshold.
plot: A character string. Specifies whether to generate a plot. Accepted values are `"bar_plot"` to generate the plot or `"no"` to return only the summary table. Defaults to `"bar_plot"`.

Value

If `plot` is set to `"no"`, the function returns a `tibble` summarizing the mean `Number_of_phosphosites` for each `Group`. If `plot` is `"bar_plot"`, the function returns a `list` with two elements:

`table`: The summary `tibble` with mean counts per group.
`plot`: A `ggplot` object of the bar plot, ready for printing.

The function will stop and return an error if the required columns are missing or the `prob_threshold` is not a valid number.

Details

The generated plot shows the mean count for each "Group" as a bar and includes jittered points representing the individual sample counts.

Examples

if (FALSE) { # \dontrun{
# Create a data frame for demonstration
data <- data.frame(
  Sample = c("p1_control", "p2_control", "p3_dose-1", "p4_dose-1", "p5_dose-2", "p6_dose-2"),
  phosphosites = c("amino_acid_S1", "amino_acid_T2", "amino_acid_Y4",
                   "amino_acid_S1", "amino_acid_T2", "amino_acid_S1"),
  Probability = c(0.95, 0.82, 0.65, 0.91, 0.73, 0.99)
)

# Get the summary table and the bar plot for a probability threshold of 0.75
results <- get_count_phosphosite(data, prob_threshold = 0.75,
plot = "bar_plot")
print(results$table)
print(results$plot)

# Get only the summary table for a probability threshold of 0.9
summary_table <- get_count_phosphosite(data, prob_threshold = 0.9,
plot = "no")
print(summary_table)
} # }