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Updates #44

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Jun 4, 2021
Merged

Updates #44

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3 changes: 1 addition & 2 deletions worked_examples/Spatial_workflows/Simple spatial workflow/Simple spatial 1 - add masks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,6 @@

str(spatial.dat, 3)

spatial.dat[[1]]$RASTERS
spatial.dat[[1]]$MASKS

###################################################################################
Expand Down Expand Up @@ -176,7 +175,7 @@

as.matrix(names(cell.dat))
cellular.cols <- names(cell.dat)[c(6:20)]
cellular.cols
as.matrix(cellular.cols)

### Arcsinh transformation

Expand Down
98 changes: 50 additions & 48 deletions worked_examples/Spatial_workflows/TIFF to FCS/TIFF to FCS.R
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
###################################################################################
### Spectre: TIFF to FCS
###################################################################################

### Load libraries

library('Spectre')

Spectre::package.check(type = 'spatial')
Spectre::package.load(type = 'spatial')

### Set PrimaryDirectory

dirname(rstudioapi::getActiveDocumentContext()$path) # Finds the directory where this script is located
Expand All @@ -23,7 +23,7 @@
setwd("data/ROIs/")
InputDirectory <- getwd()
InputDirectory

### Set MaskDirectory (ROI mask TIFFs)

setwd(PrimaryDirectory)
Expand All @@ -34,8 +34,8 @@
### Create output directory

setwd(PrimaryDirectory)
dir.create("Output - FCS files")
setwd("Output - FCS files")
dir.create("Output 1 - add masks")
setwd("Output 1 - add masks")
OutputDirectory <- getwd()
OutputDirectory

Expand All @@ -55,9 +55,9 @@
### Check channel names

for(i in rois){
setwd(InputDirectory)
setwd(i)
tiff.list[[i]] <- list.files(getwd())
setwd(InputDirectory)
setwd(i)
tiff.list[[i]] <- list.files(getwd())
}

t(as.data.frame(tiff.list))
Expand All @@ -67,12 +67,12 @@
###################################################################################

### Read in ROI channel TIFFs

setwd(InputDirectory)
spatial.dat <- read.spatial.files(rois = rois, roi.loc = getwd())

### Check results

str(spatial.dat, 3)
spatial.dat[[1]]$RASTERS

Expand All @@ -81,12 +81,12 @@
###################################################################################

### Define cell mask extension for different mask types

setwd(MaskDirectory)

all.masks <- list.files(pattern = '.tif')
as.matrix(all.masks)

### Import CELL masks

as.matrix(all.masks)
Expand All @@ -100,10 +100,11 @@
masks = cell.masks,
mask.label = 'cell.mask',
mask.ext = cell.mask.ext)

### Review data

str(spatial.dat, 3)

spatial.dat[[1]]$RASTERS
spatial.dat[[1]]$MASKS

###################################################################################
Expand All @@ -118,7 +119,6 @@

str(spatial.dat, 3)

spatial.dat[[1]]$RASTERS
spatial.dat[[1]]$MASKS

###################################################################################
Expand All @@ -131,22 +131,24 @@
dir.create('Plots - cell masks')
setwd('Plots - cell masks')

as.matrix(names(spatial.dat[[1]]$RASTERS))

base <- 'DNA1_Ir191'
mask <- 'cell.mask'

for(i in names(spatial.dat)){
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = base,
mask.outlines = 'cell.mask')
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = base,
mask.outlines = 'cell.mask')
}

###################################################################################
### Extract 'per cell' data
###################################################################################

### Extract cellular data for each cell mask

spatial.dat <- do.extract(spatial.dat, 'cell.mask')
str(spatial.dat, 3)

Expand All @@ -173,14 +175,14 @@

as.matrix(names(cell.dat))
cellular.cols <- names(cell.dat)[c(6:20)]
cellular.cols
as.matrix(cellular.cols)

### Arcsinh transformation

cell.dat <- do.asinh(cell.dat, cellular.cols, cofactor = 1)

### Invert y axis

all.neg <- function(test) -1*abs(test)

y_invert <- cell.dat[['y']]
Expand All @@ -190,7 +192,7 @@
cell.dat

### Write FCS files

setwd(OutputDirectory)
dir.create('FCS files')
setwd('FCS files')
Expand Down Expand Up @@ -224,38 +226,38 @@
setwd('Plots - expression')

for(i in plot.rois){
for(a in exp.plot){
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = a,
mask.outlines = 'cell.mask')
}
for(a in exp.plot){
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = a,
mask.outlines = 'cell.mask')
}
}

### Factor data point plots

setwd(OutputDirectory)
dir.create('Plots - data point expression')
setwd('Plots - data point expression')

for(i in plot.rois){
for(a in exp.plot){
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = a,
mask.outlines = 'cell.mask',
cell.dat = 'CellData',
cell.col = a)
}

for(a in factor.plot){
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = a,
mask.outlines = 'cell.mask',
cell.dat = 'CellData',
cell.col = a,
cell.col.type = 'factor')
}
for(a in exp.plot){
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = a,
mask.outlines = 'cell.mask',
cell.dat = 'CellData',
cell.col = a)
}
for(a in factor.plot){
make.spatial.plot(spatial.dat = spatial.dat,
image.roi = i,
image.channel = a,
mask.outlines = 'cell.mask',
cell.dat = 'CellData',
cell.col = a,
cell.col.type = 'factor')
}
}