plot.smolr_image: PLOT of SMOLR objects

In maartenpaul/SMoLR: Single Molecule Localization Microscopy visualization and analysis in R

Description

Different objects from SMoLR can be plotted using the plot() function. Depending on the type of object an image or a scatter plot will be returned.

Usage

plot.smolr_image(x, y, saturate = 0, brightness = 0, contrast = 1, rgb = F, ...)
plot.smolr_kde(x, y, saturate = 0, brightness = 0, contrast = 1, rgb = F, ...)
plot_lut.smolr_image(channel,lut)
plot.smolr_dbscan(x,hide_noise=FALSE)

Arguments

saturate	Fraction of pixels that will be saturated in the plotted image
brightness	Adjust brightness, value between 0 and 1, this will shift the pixel values with the indicated value (default=0).
contrast	Adjust contrast, pixel values are multiplied with the input value (default = 1).
rgb	Make an RGB image, default=FALSE
lut	Use a lookup table from the pals package
hide_noise	Used for a smolr_dbscan, this will hide to localizations which are not in a cluster (background/noise).

Author(s)

Optical Imaging Centre ErasmusMC Rotterdam

See Also

pals,continuous

Examples

plot(SMOLR(smolrdata))
plot(SMOLR(smolrdata),brightness = 0.9)
plot(SMOLR(smolrdata),saturate = 0.2)

plot(SMOLR_KDE(smolrdata))
plot(SMOLR_KDE(smolrdata),contrast=2)

plot(SMOLR_DBSCAN(smolrdata,MinPts=15),hide_noise = F)
plot(SMOLR_DBSCAN(smolrdata,MinPts=15),hide_noise = T)

plot_lut(SMOLR(smolrdata),channel = 1)
plot_lut(SMOLR(smolrdata),channel = 2,"warmcool")
plot_lut(SMOLR(smolrdata),channel = 3,"coolwarm")

maartenpaul/SMoLR documentation built on May 21, 2019, 10:14 a.m.