scramblase_assay_plot: scramblase_assay_plot

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/scramblase_assay_plot.R

Description

Functions for the presentation and evaluaton of dithionite scramblase assays

Usage

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scramblase_assay_input_template(path = "scramblase_assay_input_template.txt")

scramblase_assay_plot(x, scale_to = c("model", "data"),
  ppr_scale_factor = 0.65, force_through_origin = TRUE,
  generation_of_algorithm = c(2, 1), split_by_experiment = TRUE,
  r_bar = 88, sigma_r_bar = 28)

scramblase_assay_stats(x, scale_to = c("model", "data"),
  ppr_scale_factor = 0.65, force_through_origin = TRUE,
  generation_of_algorithm = c(2, 1), split_by_experiment = TRUE,
  r_bar = 88, sigma_r_bar = 28)

scramblase_assay_traces(x, ppr_scale_factor = 0.65, time_min_sec = NA_real_,
  time_max_sec = NA_real_, adjust = TRUE)

Arguments

path

character object giving the path of an empty template for a spreadsheet that can provide x.

x

data.frame or path to a tab delimited file representing it (see "Details").

scale_to

Defines the source of ymax, defaulting to model. See "Details".

ppr_scale_factor

numeric object providing a scale factor to adjust internally calculated Protein per Phospholipid (mg/mmol) ratios (PPR; see "Details").

force_through_origin

logical indicating whether to force the fitted curve(s) to penetrate the origin (defaulting to TRUE). See "Details".

generation_of_algorithm

Either 2 or 1 (numeric; defaulting to 2). See "Details".

split_by_experiment

A single logical, indicating whether or not calculations and plots will treat experimental series from different experiments separately (TRUE, default) or whether data from all experiments included is used for a single calculation/plot per experimental series (FALSE). While the former emphasizes reproducibility, the latter likely produces a more reliable fit.

r_bar

A numeric, representing the average radius of the liposomes used in the assay. Only used in generatio_of_algorithm = 2 and defaulting to 88 (see Ploier et al. 2016 for details).

sigma_r_bar

A numeric, representing the standard deviationaverage of the radius distribution of the liposomes used in the assay. Only used in generatio_of_algorithm = 2 and defaulting to 28 (see Ploier et al. 2016 for details).

time_min_sec

A single numeric. If given, scramblase_assay_traces produces a time/x axis trimmed to this value (in seconds).

time_max_sec

A single numeric. If given, scramblase_assay_traces produces a time/x axis trimmed to this value (in seconds).

adjust

A single logical, indicating whether (default) or not spectral traces to be plotted are algorithmically aligned at the time point of dithionite addition.

Details

The data.frame accepted by the majority of the functions a an R object or path to a corresponding file (x) must have the following mandatory columns:

Path:

Paths to existing and readable ASCII output files of a fluorimeter. See parse_fluorimeter_output for details and supported formats.

Protein Reconstituted (mg):

Self-explanatory.

Further (facultative) columns are:

Fluorescence Assay Vol. w/o DT (ul):

Volume of the fluorescence assay prior to addition of ditihionite (defaulting to 2000).

Fluorescence Assay Vol. with DT (ul):

Volume of the fluorescence assay after the addition ditihionite (defaulting to 2040).

Lipid in Reconstitution (mmol):

Self-explanatory. For the standard phospholipid experiment defaulting to 0.0045 (1 ml of a 4.5 mM solution).

Timepoint of Measurement (s):

The time to determine terminal fluorescence, calculated from the point when dithionite is added, in seconds, defaulting to 400).

Experiment:

Identifier for any given experiment. Used for facet_wrap during generation of ggplot output. All data with one Experiment identifier ends up on one plot/facet.

Experimental Series:

Identifier for a given series/graph (e.g. Extract and Depleted Extract). Used by color during generation of ggplot output to differentiate lines in the same plot/facet.

Based on Goren et al. (2014) and Ploier et al. (2016) data is processed as follows (the majority of the processing is split off into the internal function scramblase_assay_calculations):

Value

scramblase_assay_traces and scramblase_assay_plot return ggplot objects representing the raw fluorescence traces and a complete PPR plot, respectively. scramblaseAssayInputTemplate generates a tab-delimited ASCII file in the file system and does not provide further output. scramblaseAssayStats assembles (and prints) assay statistics as a data.frame.

Author(s)

Johannes Graumann

References

Menon, I., Huber, T., Sanyal, S., Banerjee, S., Barre, P., Canis, S., Warren, J.D., Hwa, J., Sakmar, T.P., and Menon, A.K. (2011) <DOI:10.1016/j.cub.2010.12.031>

Goren, M.A., Morizumi, T., Menon, I., Joseph, J.S., Dittman, J.S., Cherezov, V., Stevens, R.C., Ernst, O.P., and Menon, A.K. (2014) <DOI:10.1038/ncomms6115>

Ploier, B., Caro, L.N., Morizumi, T., Pandey, K., Pearring, J.N., Goren, M.A., Finnemann, S.C., Graumann, J., Arshavsky, V.Y., Dittman, J.S., Ernst, O.P., Menon, A.K. (2016). <DOI:10.1038/ncomms12832>

See Also

parse_fluorimeter_output nlsLM

Examples

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## Not run: 
library(magrittr)
library(ggplot2)
# Extract example data
analysis_dir <- file.path(tempdir(), "flippant-case-study")
extract_case_study_data(analysis_dir)
template_file <- file.path(analysis_dir, "inputTable.txt")
# Plot the spectral traces
scramblase_assay_traces(
  template_file,
  time_max_sec = 350)
# Plot the PPR plot(s) faceting by experiment
scramblase_assay_plot(template_file)
# Generate tabular results
scramblase_assay_stats(template_file)
# Plot the PPR plot(s) forgoing faceting by experiment
scramblase_assay_plot(template_file, split_by_experiment = FALSE)
# Generate tabular results
scramblase_assay_stats(template_file, split_by_experiment = FALSE)

## End(Not run)

flippant documentation built on May 1, 2019, 8:22 p.m.