View source: R/cellid_wrapper.R
cell2 | R Documentation |
Function to run CellID
cell2( arguments, cell.command = NULL, no_cores = NULL, debug_flag = 0, dry = F, encode_cellID_in_pixels = F, fill_interior_pixels = F, label_cells_in_bf = F, output_coords_to_tsv = F, ignore.stdout = T, intern = T )
arguments |
An argument data.frame, as built by rcell2::cellArgs2. |
cell.command |
Path to the binary executable (get if from https://github.com/darksideoftheshmoo/cellID-linux). Or "cellBUILTIN" for the builtin binary. |
no_cores |
Position-wise parallelization,internally capped to number of positions in cell.args. |
debug_flag |
Set to 0 to disable CellID printf messages (builtin CellID only). |
dry |
Do everything without actually running CellID, print the commands that would have been issued. |
encode_cellID_in_pixels |
Set to TRUE to write cell interior and boundary pixels with intensity-encoded CellIDs and blank the rest of the image (CellID option '-s'). |
fill_interior_pixels |
Set to TRUE to fill each cell interior area in the output image file with intensity-labeled pixels (CellID option '-i'). |
label_cells_in_bf |
Set to TRUE to enable labeling of cells with their CellID in the BF output image (CellID option '-l', default FALSE). |
output_coords_to_tsv |
Set to TRUE to write cell interior and boundary pixels data to a .tsv file in the output directory (CellID option '-m'). |
ignore.stdout |
Set to FALSE to see CellID output from a system call. |
intern |
Set to TRUE to save CellID output from a system call to a file in the "out" directories (one per position) and the commands to a file at the first "path" in the arguments data.frame. |
A dataframe with one column indicating the issued commands. Use rcell2::load_cell_data to get the results from the CellID output, typically located at the images path.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.