Plot sample traces

Plot the raw trace data

Usage

plot_traces(
  fragments_list,
  show_peaks = TRUE,
  n_facet_col = 1,
  sample_subset = NULL,
  xlim = NULL,
  ylim = NULL,
  x_axis = NULL,
  signal_color_threshold = 0.05
)

Arguments

fragments_list

A list of fragments_repeats or fragments_trace objects containing fragment data.

show_peaks

If peak data are available, TRUE will plot the peaks on top of the trace as dots.

n_facet_col

A numeric value indicating the number of columns for faceting in the plot.

sample_subset

A character vector of unique ids for a subset of samples to plot

xlim

the x limits of the plot. A numeric vector of length two.

ylim

the y limits of the plot. A numeric vector of length two.

x_axis

A character indicating what should be plotted on the x-axis, chose between size or repeats. If neither is selected, an assumption is made based on if repeats have been called.

signal_color_threshold

Threshold relative to tallest peak to color the dots (blue above, purple below).

Value

plot traces from fragments object

Details

A plot of the raw signal by bp size. Red vertical line indicates the scan was flagged as off-scale. This is in any channel, so use your best judgment to determine if it's from the sample or ladder channel.

If peaks are called, green is the tallest peak, blue is peaks above the signal threshold (default 5%), purple is below the signal threshold. If force_whole_repeat_units is used within call_repeats(), the called repeat will be connected to the peak in the trace with a horizontal dashed line.

The index peak will be plotted as a vertical dashed line when it has been set using assign_index_peaks().

Examples

fsa_list <- lapply(cell_line_fsa_list[1], function(x) x$clone())

find_ladders(fsa_list, show_progress_bar = FALSE)

fragments_list <- find_fragments(fsa_list,
  min_bp_size = 300
)

find_alleles(
  fragments_list
)

# Simple conversion from bp size to repeat size
call_repeats(
  fragments_list
)

plot_traces(fragments_list, xlim = c(105, 150))