SMOLR_PLOT: Plots single molecule datasets in a scatter plot

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

Plots single molecule datasets in a scatter plot

Usage

SMOLR_PLOT(x,y,size,color,rev.size,rev.color, xlim, ylim,px,grey,split_ch,fit,clim,slim,alpha,overlay,contrast,color_scale)
## S3 method for class 'data.frame'
SMOLR_PLOTSMOLR_PLOT(x,size,color,rev.size,rev.color, xlim, ylim,px,grey,split_ch,fit,clim,slim,alpha,overlay,contrast,color_scale)

Arguments

x	Vector of x values (nm) or data.frame containing x and y collumns
y	Vector of y values (nm)
size	Vector of variables that will be indicated by the size of the plotted points
color	Vector of variables that will be indicated by the color of the plotted points
rev.size	If FALSE small numbers will give rise to smaller points, if TRUE the higher the number the smaller the size.
rev.color	If FALSE colors will run from red to green, if TRUE colors will run from green to red
xlim	Vector containing the lower and upper limit for x values displayed
ylim	Vector containing the lower and upper limit for x values displayed
clim	Vector containing the lower and upper limit for size values displayed
slim	Vector containing the lower and upper limit for color values displayed
px	Pixelsize can used to scale the image to desirable size of points
grey	Displays the graph in a greyscale if TRUE
split_ch	If TRUE and a channel collum was present the output will be divided over multiple graphs IF FALSE a single graph will be made with containing all channels
fit	If fit is TRUE values will be scaled to fit within the plot
color_scale	Add your own color scale to the plot. The values in color are automatically scaled between the first and last color in the scale. Using adjustcolor() transparency can be added to the color scale.
alpha	A number between 0 and 1 indicating the transparancy of the plotted points
overlay	smolr_image or file location of a tiff file to which the plot will be overlayed
contrast	Value indicating what percentage of saturated pixels will be in the overlay (i.e. 1.2 will give 20 percent saturated pixes)
color_scale	vector containing a custom color scale

Author(s)

Optical Imaging Center Rotterdam

Examples

SMOLR_PLOT(smolrdata,rev.color=TRUE,size="off",split_ch=TRUE)

SMOLR_PLOT(smolrdata,color_scale = adjustcolor(c("red","green","magenta"),0.3))

overlay <- SMOLR(smolrdata)
SMOLR_PLOT(smolrdata,overlay=overlay,alpha = 0.2,size="off",,color_scale = adjustcolor(c("red","green","blue")),px=1)

ErasmusOIC/SMoLR documentation built on Aug. 20, 2024, 8:50 p.m.