plotDynamics {doblin}R Documentation

Plot barcode dynamics

Description

This function plots the dynamics of barcode frequencies over time, using either linear-scale area plots, logarithmic-scale line plots, or both. Only the most frequent barcodes are colored.

Usage

plotDynamics(
  reshaped_df,
  colored_topFreq_df,
  min_freq_threshold,
  plot_model,
  output_directory,
  input_name
)

Arguments

reshaped_df

A dataframe produced by reshapeData(), containing barcode frequencies over time.

colored_topFreq_df

A dataframe with top barcodes and their assigned color hex codes and max frequencies.

min_freq_threshold

A numeric threshold; barcodes with max frequency below this are colored gray.

plot_model

One of "linear", "logarithmic", or "both" to specify the plot type(s).

output_directory

A string specifying the directory where plots will be saved.

input_name

A string used as the base name for output files (e.g., "replicate1").

Value

No return value. Depending on the plot_model parameter:

Examples


# Load demo barcode count data
demo_file <- system.file("extdata", "demo_input.csv", package = "doblin")
input_dataframe <- readr::read_csv(demo_file, show_col_types = FALSE)

# Reshape and extract top lineages
reshaped_df <- reshapeData(input_dataframe)
top_barcodes <- fetchTop(reshaped_df, N_LINEAGES = 10)

# Load color list and assign hex codes
color_file <- system.file("extdata", "top_colors2.csv", package = "doblin")
color_df <- readr::read_csv(color_file, show_col_types = FALSE)
color_df <- color_df[1:nrow(top_barcodes), ]
colored_top <- cbind(top_barcodes, color_df)

# Plot dynamics
plotDynamics(
  reshaped_df = reshaped_df,
  colored_topFreq_df = colored_top,
  min_freq_threshold = 0.001,
  plot_model = "both",
  output_directory = tempdir(),
  input_name = "demo"
)


[Package doblin version 0.1.1 Index]