#install devtools from cran
install.packages('devtools')
#load devtools and install the package
library(devtools)
install_github("gusef/IrisSpatialFeatures")
There is a vignette included in the 'vignette' directory of the package.
Uses the default mask to define the ROI if one is included
data <- read_raw('Test ROI')
Assumes every frame of every sample has *_ROI.tif with a defined area.
data <- read_raw('Test ROI',customMask="ROI")
sample_count_density <- counts_per_mm2_sample_data_frame(data)
frame_count_density <- counts_per_mm2_data_frame(data)
sample_count <- counts_sample_data_frame(data)
frame_count <- counts_data_frame(data)
Assumes each sample and frame has *_Tumor.tif and *_Invasive_Margin.tif with defined areas
data <- read_raw('Test tumor IM mixed case copy',
readTumorAndMarginMasks=TRUE)
tumor <- extract_ROI(data,'tumor')
stroma <- extract_ROI(data,'stroma')
invasive_margin <- extract_ROI(data,'invasive_margin')
tumor_count_density <- counts_per_mm2_sample_data_frame(tumor)
stroma_count_density <- counts_per_mm2_sample_data_frame(stroma)
invasive_margin_count_density <- counts_per_mm2_sample_data_frame(invasive_margin)
Only requires *_Tumor.tif for each frame. We use it as a custom mask and don't concern ourselves with the Invasive Margine files.
tumor <- read_raw('Test tumor IM mixed case copy',
customMask='Tumor')
tumor_count_density <- counts_per_mm2_sample_data_frame(tumor)
Content type
Image
Digest
Size
1.3 GB
Last updated
about 8 years ago
docker pull vacation/irisspatialfeatures