Transform x3p surface matrix values — x3p

x3p_elemAverage() calculate the element-wise average between two surface matrices (of the same dimensions)

x3p_sd() Calculate the standard deviation of x3p surface values

x3p_filter() replace values of a surface matrix based on an element-wise conditional function

x3p_cropWS() Crop rows/columns of missing values around an x3p

x3p_to_dataFrame() Convert an x3p object to a data frame

x3p_delete() replace values in a surface matrix with NA depending on an associated mask.

Usage

x3p_elemAverage(x3p1, x3p2)

x3p_sd(..., na.rm = TRUE)

x3p_filter(x3p, cond, replacement = NA, ...)

x3p_cropWS(x3p, croppingThresh = 1)

x3p_to_dataFrame(x3p, preserveResolution = FALSE)

x3p_delete(x3p, mask_vals)

Arguments

x3p1: an x3p object
x3p2: another x3p object
...: one or more x3p objects
na.rm: logical. Should missing values be removed?
x3p: an x3p object
cond: a Boolean function whose first argument is `x`.
replacement: value to replace each element for which cond returns FALSE
croppingThresh: minimum number of non-NA pixels that need to be in a row/column for it to not be cropped out of the surface matrix
preserveResolution: a Boolean dictating whether the scan resolution is preserved in the returned data frame. If FALSE, then the x,y data frame columns will be integer-valued. Otherwise, the difference between consecutive x,y values will be equal to the scan resolution.
mask_vals: a hexidecimal color value that corresponds to indices in a mask whose indices are to be replaced in the associated surface

Details

Transform the values of a x3p surface matrix

Examples

data("K013sA1","K013sA2")

# calculates the sd for a single x3p's surface values
x3p_sd(K013sA1)
#> [1] 1.3624

# calculates the sd for the joint surface values for two x3ps
x3p_sd(K013sA1,K013sA2)
#> [1] 1.336353

# calculate optimal alignment between the two x3ps
K013sA2_aligned <- cmcR::comparison_allTogether(K013sA1,K013sA2,theta = -3,
                                                returnX3Ps = TRUE,numCells = c(1,1),
                                                maxMissingProp = .99)$alignedTargetCell[[1]]

averaged <- x3p_elemAverage(K013sA1,K013sA2_aligned)

# this will replace values that are larger (in magnitude) than one standard
# deviation of the input x3p's surface values with NA:
filtered1 <- x3p_filter(K013sA1,
                        cond = function(x,thresh) x < thresh,
                        thresh = x3p_sd(K013sA1))

# this will replace all surface matrix values between -1 and 1 with 0
filtered2 <- x3p_filter(K013sA1,cond = function(x) abs(x) < 1,replacement = 0)

# exaggerated cropping for the sake of an example
cropped <- x3p_cropWS(K013sA1,croppingThresh = 100)

x3pPlot(K013sA1,K013sA2_aligned,averaged,filtered1,filtered2,cropped,
        x3pNames = c("K01sA1","K013sA2 Aligned","Averaged","Filtered1","Filtered2","Cropped"))
#> Error in purrr::map_chr(x3pList, class): ℹ In index: 2.
#> ℹ With name: surface.matrix.
#> Caused by error:
#> ! Result must be length 1, not 2.