Package 'blotbench'

Manually apply transforms to imgs

Description

While functions like wb_present will automatically apply transformations, this function allows you to apply them manually.

Usage

apply_transforms(wb)

Arguments

wb	A wb object

---

Get or set column annotation for a wb object

Description

Get or set column annotation for a wb object

Usage

col_annot(x)

col_annot(x) <- value

Arguments

x	A wb object
value	A data.frame with each column representing a variable, and each row representing a lane in the blot. NOTE: the order of the rows should annotate the lanes left-to-right AFTER image manipulation, which might include mirroring.

---

Get or set images for a wb object

Description

Get or set images for a wb object

Usage

imgs(x)

imgs(x) <- value

wb_add_img(x, imgs, names)

Arguments

x	A wb object
value	Unused.
imgs	A magick-image containing one or more images
names	A character vector of names with length equal to imgs. Can be NULL if row_annot is NULL

Details

Note that ⁠imgs<-⁠ is unused - add images using wb_add_img

---

Test if the object is a wb

Description

Test if the object is a wb

Usage

is_wb(x)

Arguments

x	Object to be tested

Value

Logical. TRUE if object inherits from the wb class

---

Get or set row annotation for a wb object

Description

Get or set row annotation for a wb object

Usage

row_annot(x)

row_annot(x) <- value

Arguments

x	A wb object
value	Either a data.frame with a single column name, or a character vector

---

Get or set transforms of a wb object

Description

Get or set transforms of a wb object

Usage

transforms(x)

transforms(x) <- value

Arguments

x	A wb object
value	A data.frame with the same number of rows as row_annot, if not null, and with columns width, height, xpos, ypos, rotate, and flip

---

Create a wb object

Description

Create a wb object

Usage

wb(imgs, col_annot = NULL, row_annot = NULL, transforms = NULL)

Arguments

imgs	A vector of magick-images
col_annot	A data.frame, where each row is a lane and each column is a condition
row_annot	A data.frame, where each row is a band and the first column contains band names
transforms	A data.frame, where each row contains image transformation parameters for an item in imgs. Typically left blank unless you know what you're doing

---

Convert a .scn file to another format

Description

The BioRad ChemiDoc produces .scn files that can be converted to .tif(f) files using bfconvert.

Usage

wb_convert_scn(file, dest_name = NULL, overwrite = FALSE)

Arguments

file	Character. Path to the file to be converted.
dest_name	Character. File name and path to save to. If not supplied, will be same name and location as input, but with a .tif extension.
overwrite	Logical. Should the file be overwritten if it already exists?

Details

This function requires bftools to be installed

Value

Path to the saved file

Examples

## Not run: 
wb_convert_scn("path/to/file.scn", dest_name = "~/new/path.tif")

## End(Not run)

---

Render a wb object into an image

Description

This function takes a wb object and (optionally) row and column annotations and produces an image from them.

Usage

wb_present(wb)

Arguments

wb	A wb object with at least images and transformations

---

Interactively edit blots

Description

This function helps generate code needed to transform a blot to your specifications via a Shiny app

Usage

wb_visual_edit(wb)

Arguments

wb	A wb object

---