plotRaw: Plot TIFF, cell contours and/or spot localization on the...

In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data

Plot TIFF, cell contours and/or spot localization on the original x/y space.

Description

To check segmentation, view TIFF images and/or show the localization of spots inside cells. ggplot2-based, so other geoms and theme layers can be added.

Usage

plotRaw(tiffdata,
        meshdata,
        spotdata,
        frameN = 1,
        xrange,
        yrange,
        viridisoption = "inferno",
        meshcolor = "white",
        spotcolor = "yellow",
        valuerange,
        legend=FALSE)

Arguments

tiffdata	(list of) dataframe(s) containing *x* and *y* coordinates of pixels and their *values*. Can be generated by loading a TIFF into R using bactMAP::extr_OriginalStack()
meshdata	dataframe containing (at least) *X* and *Y* coordinates of cells outlines, the *frame* number of the image and *cell* numbers.
spotdata	dataframe containing (at least) *x* and *y* coordinates of spots and the *frame* number of the image.
frameN	number of the frame to be displayed. default = 1.
xrange	vector with minimum and maximum x coordinates to be displayed (by default all is shown).
yrange	vector with minimum and maximum y coordinates to be displayed (by default all is shown).
viridisoption	one of the viridis color scale options (default = "inferno") for the displayed TIFF. options: "magma", "viridis", "cividis", "plasma" and "inferno"
meshcolor	color of the cell outlines. default = "white"
spotcolor	color for displayed spots. default = "yellow"
valuerange	vector with minumum and maximum pixel values to show TIFF, use this option to increase contrast
legend	displays a figure legend when legend==TRUE

Value

A plot showing either a TIFF, mesh outlines, spot coordinates or a combination of the three.

Author(s)

Renske van Raaphorst

See Also

extr_Original, viridis

Examples

## Not run: 

#load TIF image from BactMAP examples. go to veeninglab.com/bactmap to download.

TIF_image <- file.choose()

#use extr_-function to turn into list of dataframes

TIF_df <- bactMAP::extr_OriginalStack(TIF_image)

#plot image
plotRaw(TIF_image)

require(ggplot2)
#zoom in and add title
plotRaw(TIF_image, xrange=(c(200,500)), yrange=c(400,600)) + ggplot2::ggtitle("This is a TIF image")

## End(Not run)

vrrenske/shinyspots documentation built on Oct. 28, 2023, 12:26 p.m.