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Plots poly(A) tail length (or estimated non-A position) distribution in analyzed sample(s).

Source: R/ninetails_plotting_functions.R
plot_tail_distribution.Rd

This function plots distributions of either poly(A) tail lengths or estimated non-A residues' positions across the dataset using the user-predefned grouping variable (e.g. samples, conditions etc.). The grouping variable must be a column within the input dataset passed to the function.

Usage

plot_tail_distribution(
  input_data,
  variable_to_plot = "polya_length",
  grouping_factor = NA,
  max_length = NA,
  value_to_show = NA,
  ndensity = T,
  title = F
)

Arguments

input_data

the ninetails pipeline output data preprocessed with the merge_nonA_tables function or residue_data or other suitable data

variable_to_plot

[character] string, the variable to be plotted defined by the user. By default (if not provided by the user) the polya_length would be plotted. Note that this variable has to be the column of input_data.

grouping_factor

[character] string, the grouping variable defined by the user. Note that this variable has to be the column of input_data.

max_length

[numeric] maximum length of plotted tail data

value_to_show

[character] string; one of the measures of central tendency: either the "mode", the "median" or the "mean" value, which user wants to be displayed on the plot. By default, none is specified.

ndensity

logical [TRUE/FALSE]. If TRUE, the normalized density would be shown. If false - the data would not be normalized. It is set to "TRUE" by default.

title

logical [TRUE/FALSE]. If TRUE, the title + subtitles would be displayed. If not - the title & subtitle would not be visible.

Value

a ggplot object

Details

User can specify this in samples_table if the ninetails pipeline output is intended to be loaded into R session by read_residue_multiple and read_class_multiple functions or added manually by other means.

The function takes as an input merged ninetails' output dataset, which can be produced with the merge_nonA_tables function.

The function allows to mark measures of central tendency, either mean, median or mode (as vertical dashed line). One of these values may be shown on the plot with additional caption in lower right corner. This is an optional feature.

Mean and median are computed using base R functions.

The mode value (if specified by value_to_show argument) is computed using the get_mode function. This is a custom helper function written based on this thread: https://stackoverflow.com/questions/2547402/how-to-find-the-statistical-mode

This returns the density mode for normalized data to avoid unexpected results (messed-up plots) which may occur if the distribution is bi- or multimodal.

This is the ninetails' implementation of plot_polya_distribution() from Nanotail backage by P. Krawczyk (smaegol) written under author's permission.

The original code is available here: https://github.com/smaegol/nanotail/blob/master/R/polya_plots.R

The function was simplified & adjusted to ninetails' naming convention to avoid confusion & overwriting, if both packages are loaded in the same R session.

Examples

if (FALSE) { # \dontrun{

plt <- ninetails::plot_tail_distribution(input_data = merged_nonA_tables,
                                         variable_to_plot = "polya_length",
                                         grouping_factor = "group",
                                         max_length = 200,
                                         value_to_show = "median",
                                         ndensity=T,
                                         title=F)


} # }