save_dye_screen_figs: Save dye screen figures

In taiawu/dsfworld_package: Visualizes and Analyzes Differential Scanning Fluorimetry Data

Save dye screen figures

Description

The save_dye_screen_figs() function is used to quickly generate and save three of the four standard raw data figures in a dye screening workflow. See the 'Details' section below for more information on each of these plots.

Usage

save_dye_screen_figs(tidied_screen, plot_type, hits, ...)

Arguments

tidied_screen	a tibble containing raw data from a dye screen, both protein and buffer, e.g. as output by the tidy_dye_screen() function.
plot_type	type of figure to create. Options: "full_screen", "divided", "hits_by_channel", which generate and save figures created by the save_full_screen() function, the save_stacked_screen() function, and the save_stacked_hits() function respectively.
hits	a tibble containing hit assignments for each dye. Must have columns "dye" and "assignment", described below: "dye", a character column containing the names of all of the dyes tested in the experiment. In order for a dye to be displayed in this plot, its name in this dataframe must match its name in the tidied_screen dataframe exactly. Matches are case- and punctuation-sensitive. (e.g. a dye named "L045" in this tibble will match only to a dye named "L045" in the tidied_screen tibble; it will not match to "l045", "L45", "L-045", etc.). "assignment", a character column containing the assignment of how a given dye behaved with screened protein. These assignments must be supplied by the user. Assignments can be determined either manually, or with assistance using the hit-calling tools in this package (in development as of August 2021). Possible assignments are: "hit", "sensitive", and "none", which correspond to the following judgements: "hit", any dye which appears to detect the melting of the protein of interest, while having minimal temperature-sensitive fluorescence in the absence of protein. "sensitive", a less stringent category than 'hit'. Useful for dyes where definition as a "hit" isn't quite warranted, but which demonstrating some fluorescent response to the protein (over buffer) which could be potentially interesting. Common reasons for a a dye to receive a "senstive" assignment detection of non-cannonical transitions, and/or detecting a cannonical transtion, but doing so with far weaker signal than dyes called as 'hits'. In particular, the "sensitive" assignment is useful for flagging dyes which may be interesting for follow-up later, or fleshing out SAR of the hit dyes for a given protein. "none", an assignment given to dyes which showed no major difference between a DSF run with or without the protein, suggesting no fluorescent response to the protein of interest at any temperature.
...	additional arguments passed to the save_full_screen() function, the save_stacked_screen() function, or the save_stacked_hits() function. Common use could be to specify a directory to save the output plot, via .save_path.

Details

The three plots which can be generating using save_dye_screen_figs() are:

1. all raw data, with no assignments displayed. Used for calling hits, as created by the save_full_screen() function.

2. all raw data, with distinct sub-plots containing dyes given each assignment–hit, sensitive, or none–as created by the save_stacked_screen() function.

3. raw data for just dyes assigned to "hit" and "sensitive" categories, with data collected for each dye displayed in a separate row, and data for the raw data collected for that dye in each fluorescent channel displayed in a separate colummn, as created by the save_stacked_hits() function

4. Not accessed though this function. For reference, the fourth plot displays the hit and/or sensitive dyes, in specific channels, carried through model fitting and tma extraction, alongside the results of the model fitting and tma extraction.

Value

if assigned to an object, returns a ggproto object. Also saves the figure.

taiawu/dsfworld_package documentation built on June 18, 2024, 5:39 a.m.