Description Usage Arguments Details Examples
Select grid of interest from a tissue
1 2 3 |
data |
Input data in class MolDiaISS. Output of readISS. |
gridtype |
type of grid to plot. Default is "rect". See details. |
nx, ny |
Numbers of rectangular quadrats in the x and y directions |
grid_id |
Grid to select. Default id NULL. |
roifile |
Name of the file that contain ROI. csv formate. Most important is, data points should be in clockwise or anti-clockwise order. |
roi.id |
Column name in roifile file that contain ROI id |
roi.x, roi.y |
X and Y axis name in roifile file. |
main |
Main title. |
gridtype parameter can have 4 values : "hexa", "rect", "roifile" and "roi"
1. "hexa" will create hexagonal grid and number of grid is based on nx parameter and grid_id will select grid of interest.
2. "rect" will create rectangular grid and number of grid is based on nx parameter and grid_id will select grid of interest.
3. "roifile" will require a file input in csv formate in the parameter "roifile". The input file must have at least 3 column of ROI id, x-axis, y-axis. The parameter "roi.id", "roi.x" and "roi.y" will be the name input of corresponding column.
4. "roi" will select ROI more interactively. One cal select ROI on the image by pointer.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # Read ISS data
ex_data <- readISS(file = system.file("extdata", "Hypocampus_left.csv", package="MolDia"),cellid = "CellId", centX = "centroid_x", centY = "centroid_y", rpc = 3)
# Select hexagonal and rectangular ROI
mygrid <- ISS_roi(data = ex_data, nx = 8,gridtype = "hexa", main = "Hexagonal ROI on tissue")
mygrid <- ISS_roi(data = ex_data, nx = 8,gridtype = "rect", main = "Rectangular ROI on tissue")
mygrid <- ISS_roi(data = ex_data, nx = 8,gridtype = "rect", grid_id = c(6,16,20,8,17,21))
# Selected ROI from a pre selected ROI file
ex_data <- readISS(file = system.file("extdata", "CellBlobs_ROI.csv", package="MolDia"),
cellid = "CellID", centX = "centroidX", centY = "centroidY")
mygrid <- ISS_roi(data = ex_data, nx = 6, gridtype = "roifile",
roifile = system.file("extdata", "polygon_coordinates.csv", package="MolDia"),
roi.id = "Polygon_id", roi.x ="x_coordiates" , roi.y = "y_coordinates", grid_id = c(1,2,5,6),
main = "Selected ROI on tissue")
# Select ROI interactively by user
mygrid <- ISS_roi(data = ex_data, gridtype = "roi")
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