MolDia: Single cell In-Situ sequencing (ISS) data analysis

Description Usage Arguments Details Examples

Select grid of interest from a tissue

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ISS_roi(data, gridtype = "rect", nx = 6, ny = nx, grid_id = NULL,
  roifile = NULL, roi.id = NULL, roi.x = NULL, roi.y = NULL,
  main = "ROI on tissue")

`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.

# 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")