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Fix ladders interactively

fix_ladders_interactive.Rd

An app for fixing ladders

Usage

fix_ladders_interactive(fragment_trace_list)

Arguments

fragment_trace_list

A list of fragments_trace objects containing fragment data

Value

interactive shiny app for fixing ladders

Details

This function helps you fix ladders that are incorrectly assigned. Run fix_ladders_interactive() and provide output from find_ladders. In the app, for each sample, click on line for the incorrect ladder size and drag it to the correct peak.

Once you are satisfied with the ladders for all the broken samples, click the download button to generate a file that has the ladder correction data. Read this file back into R using readRDS, then use fix_ladders_manual() and supply the ladder correction data as ladder_df_list. This allows the manually corrected data to be saved and used within a script so that the correct does not need to be done every time. An example of what you would need to do:

ladder_df_list <- readRDS('path/to/exported/data.rds') test_ladders_fixed <- fix_ladders_manual(test_ladders_broken, ladder_df_list)

See also

fix_ladders_manual(), find_ladders()

Examples

fsa_list <- lapply(cell_line_fsa_list["20230413_A08.fsa"], function(x) x$clone())

find_ladders(fsa_list, show_progress_bar = FALSE)

# to create an example, lets brake one of the ladders
brake_ladder_list <-  list(
   "20230413_A08.fsa" = data.frame(
     size = c(35, 50, 75, 100, 139, 150, 160, 200, 250, 300, 340, 350, 400, 450, 490, 500),
     scan = c(1544, 1621, 1850, 1912, 2143, 2201, 2261, 2506, 2805, 3135, 3380, 3442, 3760, 
              4050, 4284, 4332)
   )
 )

fix_ladders_manual(
  fsa_list,
  brake_ladder_list
)
#> Fixing ladder for 20230413_A08.fsa
#> Warning: sample 20230413_A08.fsa has badly fitting ladder for bp sizes: 35-75, 50-100, 75-139

plot_ladders(fsa_list)



if (interactive()) {
  fix_ladders_interactive(fsa_list)
}

# once you have corrected your ladders in the app, 
# export the data for incorporation into the script.
# You can then re-import the data and fix ladders as described in the help details.