afm_trim: Trim extreme values from afm maps

In will-r-chase/afmr: Visualization and Analysis of AFM Images

Description

This function will floor extreme values from an afm map. You can inspect the distribution of values in an afm map with 'afm_hist()' and then trim extreme values either by quantile or specific cutoff. By default the cutoffs will be set to the upper 97.5 you can set the minimum and maximum values specifically using the 'min' and 'max' arguments. The trimmed data will be added to your afm_scan object under 'maps' as eg. Height_Sensor_matrix_trimmed. The trimmed data should never be used for calculation, only to improve image quality.

Usage

afm_trim(data = NULL, matrix = NULL, lower = 0.025, upper = 0.975,
  min = NULL, max = NULL)

Arguments

data	an "afm_scan" data object
matrix	the name of the afm map you want to trim
lower	the lower quantile (default 0.025)
upper	the upper quantile (default 0.975)
min	the minimum value cutoff (overrides quantile)
max	the maximum value cutoff (overrides quantile)

Value

an "afm_scan" data object with the trimmed matrix added under 'maps'

Examples

load("data/half_um_scan.rda")
afm_trim(half_um_scan, matrix = "Height_Sensor_matrix")

will-r-chase/afmr documentation built on May 9, 2019, 4:11 p.m.