I obtained a rectangular sort of image when I subset shapefile on the raster image. I want to get exact irregular shaped image so that I can proceed my classification to that particular area (B is my raster image):

boundryfile<-readOGR(dsn="E:\\FYP guide\\SUPARCO 2013\\Jamal Garhi",layer="Jamal Garhi")

R and raster crops to a bounding box so you will need to also mask to only retain the area of interest. Mask works by setting values inside or outside of a shape to a value usually NA in this context. See raster::mask command

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