update methods-ext.R #27
Conversation
jiajic
commented
Sep 19, 2023
jiajic
commented
- fixes note in rmdcheck
- increment version
fixes note in rmdcheck
catch up to main
increment version
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
|
|
||
| return(stereo) | ||
| # data.table vars | ||
| genes = y = sdimx = sdimy = cell_ID = count = NULL |
Check warning
Code scanning / lintr
local variable 'sdimx' assigned but may not be used Warning
|
|
||
| return(stereo) | ||
| # data.table vars | ||
| genes = y = sdimx = sdimy = cell_ID = count = NULL |
Check warning
Code scanning / lintr
local variable 'sdimy' assigned but may not be used Warning
|
|
||
| return(stereo) | ||
| # data.table vars | ||
| genes = y = sdimx = sdimy = cell_ID = count = NULL |
Check warning
Code scanning / lintr
local variable 'count' assigned but may not be used Warning
| bin_size)) | ||
| exprDT = data.table::as.data.table(geneExpData[['expression']]) | ||
| exprDT$count = as.integer(exprDT$count) | ||
| setorder(exprDT, x, y) # sort by x, y coords (ascending) |
Check warning
Code scanning / lintr
no visible binding for global variable 'x' Warning
| # 2. create spatial locations | ||
| if(isTRUE(verbose)) wrap_msg('2. create spatial_locations... \n') | ||
| cell_locations = unique(exprDT[,c('x','y')], by = c('x', 'y')) | ||
| cell_locations[, bin_ID := as.factor(seq_along(1:nrow(cell_locations)))] |
Check warning
Code scanning / lintr
no visible binding for global variable 'bin_ID' Warning
| # 2. create spatial locations | ||
| if(isTRUE(verbose)) wrap_msg('2. create spatial_locations... \n') | ||
| cell_locations = unique(exprDT[,c('x','y')], by = c('x', 'y')) | ||
| cell_locations[, bin_ID := as.factor(seq_along(1:nrow(cell_locations)))] |
Check warning
Code scanning / lintr
1:nrow(...) is likely to be wrong in the empty edge case. Use seq_len(nrow(...)) instead. Warning
| if(isTRUE(verbose)) wrap_msg('2. create spatial_locations... \n') | ||
| cell_locations = unique(exprDT[,c('x','y')], by = c('x', 'y')) | ||
| cell_locations[, bin_ID := as.factor(seq_along(1:nrow(cell_locations)))] | ||
| cell_locations[, cell_ID := paste0('cell_', bin_ID)] |
Check warning
Code scanning / lintr
no visible binding for global variable 'bin_ID' Warning
| # 3. create expression matrix | ||
| if(isTRUE(verbose)) wrap_msg('3. create expression matrix... \n') | ||
| exprDT[, genes := as.character(rep(x = geneDT$gene, geneDT$count))] | ||
| exprDT[, gene_idx := as.integer(factor(exprDT$genes, |
Check warning
Code scanning / lintr
no visible binding for global variable 'gene_idx' Warning
| levels = unique(exprDT$genes)))] | ||
|
|
||
| # merge on x,y and populate based on bin_ID values in cell_locations | ||
| exprDT[cell_locations, cell_ID := i.bin_ID, on = .(x, y)] |
Check warning
Code scanning / lintr
no visible binding for global variable 'i.bin_ID' Warning
| levels = unique(exprDT$genes)))] | ||
|
|
||
| # merge on x,y and populate based on bin_ID values in cell_locations | ||
| exprDT[cell_locations, cell_ID := i.bin_ID, on = .(x, y)] |
Check warning
Code scanning / lintr
no visible binding for global variable 'x' Warning
