Using synapsis
packages = c("rmarkdown","BiocManager","imager")
package.check <- lapply(
packages,
FUN = function(x) {
if (!require(x, character.only = TRUE)) {
install.packages(x, dependencies = TRUE)
library(x, character.only = TRUE)
}
}
)
## Loading required package: rmarkdown
## Loading required package: BiocManager
## Loading required package: imager
## Loading required package: magrittr
##
## Attaching package: 'imager'
## The following object is masked from 'package:magrittr':
##
## add
## The following objects are masked from 'package:stats':
##
## convolve, spectrum
## The following object is masked from 'package:graphics':
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## frame
## The following object is masked from 'package:base':
##
## save.image
library(knitr)
library(rmarkdown)
#BiocManager::install("EBImage")
library(EBImage)
##
## Attaching package: 'EBImage'
## The following objects are masked from 'package:imager':
##
## channel, dilate, display, erode, resize, watershed
library(ggplot2)
path = "~/Documents/svi/imaging/data-folder/test-folder/all-WT"
files <- list.files(path)
setwd("~/Documents/synapsis/synapsis/R")
source("auto_crop.R")
# call routine to crop images, and display their "cell number"
crop(files, path)
## [1] "cell count for above crop is"
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## List of 2
## $ message: chr "subscript out of bounds"
## $ call : language slot(noise_gone, ".Data")[ix, iy, drop = FALSE]
## - attr(*, "class")= chr [1:3] "simpleError" "error" "condition"
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## List of 2
## $ message: chr "only 0's may be mixed with negative subscripts"
## $ call : language slot(noise_gone, ".Data")[ix, iy, drop = FALSE]
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## List of 2
## $ message: chr "subscript out of bounds"
## $ call : language slot(noise_gone, ".Data")[ix, iy, drop = FALSE]
## - attr(*, "class")= chr [1:3] "simpleError" "error" "condition"
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## List of 2
## $ message: chr "only 0's may be mixed with negative subscripts"
## $ call : language slot(noise_gone, ".Data")[ix, iy, drop = FALSE]
## - attr(*, "class")= chr [1:3] "simpleError" "error" "condition"
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## List of 2
## $ message: chr "only 0's may be mixed with negative subscripts"
## $ call : language slot(noise_gone, ".Data")[ix, iy, drop = FALSE]
## - attr(*, "class")= chr [1:3] "simpleError" "error" "condition"
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## Warning in .local(object, ...): frame 1 cannot be normalized as its diff(range)
## is 0
## Warning in .local(object, ...): frame 2 cannot be normalized as its diff(range)
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## Warning in .local(object, ...): frame 3 cannot be normalized as its diff(range)
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## [1] "out of"
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## [1] "we got"
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## [1] "viable cells"
# Call for KO folder, call for WT folder.
# call same routine, but excluding those which are cropped badly.