SMOLR_PLOT: Plots single molecule datasets in a scatter plot

Usage Arguments Author(s) Examples

Usage

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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

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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)

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