lintr-bot
commented
4 years ago R/scrubletDoubletDetection.R:2:1: style: Lines should not be more than 80 characters.
#' @description Builds k-nearest neighbors using simulated doublets to estimate likelihood of doublets
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:4:1: style: Lines should not be more than 80 characters.
#' @param genes full path to a gene list usually included in the raw sequecing folder
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:5:1: style: Lines should not be more than 80 characters.
#' @param output full path to an output directory of preference. All plots, output files and log files will be written here
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:6:1: style: Lines should not be more than 80 characters.
#' @param ... Any of expected_doublet_rate,min_counts,min_cells, min_gene_variability_pctl, n_prin_comps,umap_n_neighbors, min_dist, angle,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:7:1: style: Lines should not be more than 80 characters.
# tsne_n_neighbors, n_iter, umap_order_points, tsne_order_points, fa_order_points. Provided optionally as keyword arguments. Refer scrublet documentation for details
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:10:1: style: Lines should not be more than 80 characters.
#' runScrublet(counts_matrix=mtx,genes=genes,output=outpath,expected_doublet_rate=0.2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:15:39: style: Commas should always have a space after.
runScrublet <- function(counts_matrix,genes,output,...)
^R/scrubletDoubletDetection.R:15:45: style: Commas should always have a space after.
runScrublet <- function(counts_matrix,genes,output,...)
^R/scrubletDoubletDetection.R:15:52: style: Commas should always have a space after.
runScrublet <- function(counts_matrix,genes,output,...)
^R/scrubletDoubletDetection.R:16:1: style: Opening curly braces should never go on their own line and should always be followed by a new line.
{
^R/scrubletDoubletDetection.R:16:2: style: Trailing whitespace is superfluous.
{
^R/scrubletDoubletDetection.R:18:1: style: Use spaces to indent, not tabs.
## Get user defined keyword arguments. If undefined, set defaults
^R/scrubletDoubletDetection.R:19:1: style: Use spaces to indent, not tabs.
mc <- as.list(sys.call())
^R/scrubletDoubletDetection.R:20:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['expected_doublet_rate']])) { edr <- mc$expected_doublet_rate } else { edr <- 0.06 }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:20:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['expected_doublet_rate']])) { edr <- mc$expected_doublet_rate } else { edr <- 0.06 }
^R/scrubletDoubletDetection.R:20:19: style: Only use double-quotes.
if (!is.null(mc[['expected_doublet_rate']])) { edr <- mc$expected_doublet_rate } else { edr <- 0.06 }
^~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:20:47: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['expected_doublet_rate']])) { edr <- mc$expected_doublet_rate } else { edr <- 0.06 }
^R/scrubletDoubletDetection.R:20:81: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['expected_doublet_rate']])) { edr <- mc$expected_doublet_rate } else { edr <- 0.06 }
^R/scrubletDoubletDetection.R:20:88: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['expected_doublet_rate']])) { edr <- mc$expected_doublet_rate } else { edr <- 0.06 }
^R/scrubletDoubletDetection.R:20:102: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['expected_doublet_rate']])) { edr <- mc$expected_doublet_rate } else { edr <- 0.06 }
^R/scrubletDoubletDetection.R:21:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['min_counts']])) { mincounts <- mc$min_counts } else { mincounts <- 2 }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:21:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['min_counts']])) { mincounts <- mc$min_counts } else { mincounts <- 2 }
^R/scrubletDoubletDetection.R:21:19: style: Only use double-quotes.
if (!is.null(mc[['min_counts']])) { mincounts <- mc$min_counts } else { mincounts <- 2 }
^~~~~~~~~~~~R/scrubletDoubletDetection.R:21:36: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_counts']])) { mincounts <- mc$min_counts } else { mincounts <- 2 }
^R/scrubletDoubletDetection.R:21:65: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_counts']])) { mincounts <- mc$min_counts } else { mincounts <- 2 }
^R/scrubletDoubletDetection.R:21:72: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_counts']])) { mincounts <- mc$min_counts } else { mincounts <- 2 }
^R/scrubletDoubletDetection.R:21:89: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_counts']])) { mincounts <- mc$min_counts } else { mincounts <- 2 }
^R/scrubletDoubletDetection.R:22:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['min_cells']])) { mincells <- mc$min_cells } else { mincells <- 3 }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:22:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['min_cells']])) { mincells <- mc$min_cells } else { mincells <- 3 }
^R/scrubletDoubletDetection.R:22:19: style: Only use double-quotes.
if (!is.null(mc[['min_cells']])) { mincells <- mc$min_cells } else { mincells <- 3 }
^~~~~~~~~~~R/scrubletDoubletDetection.R:22:35: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_cells']])) { mincells <- mc$min_cells } else { mincells <- 3 }
^R/scrubletDoubletDetection.R:22:62: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_cells']])) { mincells <- mc$min_cells } else { mincells <- 3 }
^R/scrubletDoubletDetection.R:22:69: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_cells']])) { mincells <- mc$min_cells } else { mincells <- 3 }
^R/scrubletDoubletDetection.R:22:85: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_cells']])) { mincells <- mc$min_cells } else { mincells <- 3 }
^R/scrubletDoubletDetection.R:23:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['min_gene_variability_pctl']])) { mingenevarpctl <- mc$min_gene_variability_pctl } else { mingenevarpctl <- 85 }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:23:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['min_gene_variability_pctl']])) { mingenevarpctl <- mc$min_gene_variability_pctl } else { mingenevarpctl <- 85 }
^R/scrubletDoubletDetection.R:23:19: style: Only use double-quotes.
if (!is.null(mc[['min_gene_variability_pctl']])) { mingenevarpctl <- mc$min_gene_variability_pctl } else { mingenevarpctl <- 85 }
^~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:23:51: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_gene_variability_pctl']])) { mingenevarpctl <- mc$min_gene_variability_pctl } else { mingenevarpctl <- 85 }
^R/scrubletDoubletDetection.R:23:100: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_gene_variability_pctl']])) { mingenevarpctl <- mc$min_gene_variability_pctl } else { mingenevarpctl <- 85 }
^R/scrubletDoubletDetection.R:23:107: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_gene_variability_pctl']])) { mingenevarpctl <- mc$min_gene_variability_pctl } else { mingenevarpctl <- 85 }
^R/scrubletDoubletDetection.R:23:130: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_gene_variability_pctl']])) { mingenevarpctl <- mc$min_gene_variability_pctl } else { mingenevarpctl <- 85 }
^R/scrubletDoubletDetection.R:24:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['n_prin_comps']])) { nprincomps <- as.integer(mc$n_prin_comps) } else { nprincomps <- as.integer(30) }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:24:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['n_prin_comps']])) { nprincomps <- as.integer(mc$n_prin_comps) } else { nprincomps <- as.integer(30) }
^R/scrubletDoubletDetection.R:24:19: style: Only use double-quotes.
if (!is.null(mc[['n_prin_comps']])) { nprincomps <- as.integer(mc$n_prin_comps) } else { nprincomps <- as.integer(30) }
^~~~~~~~~~~~~~R/scrubletDoubletDetection.R:24:38: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['n_prin_comps']])) { nprincomps <- as.integer(mc$n_prin_comps) } else { nprincomps <- as.integer(30) }
^R/scrubletDoubletDetection.R:24:82: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['n_prin_comps']])) { nprincomps <- as.integer(mc$n_prin_comps) } else { nprincomps <- as.integer(30) }
^R/scrubletDoubletDetection.R:24:89: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['n_prin_comps']])) { nprincomps <- as.integer(mc$n_prin_comps) } else { nprincomps <- as.integer(30) }
^R/scrubletDoubletDetection.R:24:120: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['n_prin_comps']])) { nprincomps <- as.integer(mc$n_prin_comps) } else { nprincomps <- as.integer(30) }
^R/scrubletDoubletDetection.R:25:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['umap_n_neighbors']])) { umapneighbors <- as.integer(mc$umap_n_neighbors) } else { umapneighbors <- as.integer(10) }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:25:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['umap_n_neighbors']])) { umapneighbors <- as.integer(mc$umap_n_neighbors) } else { umapneighbors <- as.integer(10) }
^R/scrubletDoubletDetection.R:25:19: style: Only use double-quotes.
if (!is.null(mc[['umap_n_neighbors']])) { umapneighbors <- as.integer(mc$umap_n_neighbors) } else { umapneighbors <- as.integer(10) }
^~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:25:42: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['umap_n_neighbors']])) { umapneighbors <- as.integer(mc$umap_n_neighbors) } else { umapneighbors <- as.integer(10) }
^R/scrubletDoubletDetection.R:25:93: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['umap_n_neighbors']])) { umapneighbors <- as.integer(mc$umap_n_neighbors) } else { umapneighbors <- as.integer(10) }
^R/scrubletDoubletDetection.R:25:100: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['umap_n_neighbors']])) { umapneighbors <- as.integer(mc$umap_n_neighbors) } else { umapneighbors <- as.integer(10) }
^R/scrubletDoubletDetection.R:25:134: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['umap_n_neighbors']])) { umapneighbors <- as.integer(mc$umap_n_neighbors) } else { umapneighbors <- as.integer(10) }
^R/scrubletDoubletDetection.R:26:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['min_dist']])) { mindist <- mc$min_dist } else { mindist <- 0.3 }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:26:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['min_dist']])) { mindist <- mc$min_dist } else { mindist <- 0.3 }
^R/scrubletDoubletDetection.R:26:19: style: Only use double-quotes.
if (!is.null(mc[['min_dist']])) { mindist <- mc$min_dist } else { mindist <- 0.3 }
^~~~~~~~~~R/scrubletDoubletDetection.R:26:34: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_dist']])) { mindist <- mc$min_dist } else { mindist <- 0.3 }
^R/scrubletDoubletDetection.R:26:59: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_dist']])) { mindist <- mc$min_dist } else { mindist <- 0.3 }
^R/scrubletDoubletDetection.R:26:66: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['min_dist']])) { mindist <- mc$min_dist } else { mindist <- 0.3 }
^R/scrubletDoubletDetection.R:26:83: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['min_dist']])) { mindist <- mc$min_dist } else { mindist <- 0.3 }
^R/scrubletDoubletDetection.R:27:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['angle']])) { ang <- mc$angle } else { ang <- 0.9 }
^R/scrubletDoubletDetection.R:27:19: style: Only use double-quotes.
if (!is.null(mc[['angle']])) { ang <- mc$angle } else { ang <- 0.9 }
^~~~~~~R/scrubletDoubletDetection.R:27:31: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['angle']])) { ang <- mc$angle } else { ang <- 0.9 }
^R/scrubletDoubletDetection.R:27:49: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['angle']])) { ang <- mc$angle } else { ang <- 0.9 }
^R/scrubletDoubletDetection.R:27:56: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['angle']])) { ang <- mc$angle } else { ang <- 0.9 }
^R/scrubletDoubletDetection.R:27:69: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['angle']])) { ang <- mc$angle } else { ang <- 0.9 }
^R/scrubletDoubletDetection.R:28:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['tsne_n_neighbors']])) { tsneneighbors <- as.integer(mc$tsne_n_neighbors) } else { tsneneighbors <- as.integer(5) }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:28:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['tsne_n_neighbors']])) { tsneneighbors <- as.integer(mc$tsne_n_neighbors) } else { tsneneighbors <- as.integer(5) }
^R/scrubletDoubletDetection.R:28:19: style: Only use double-quotes.
if (!is.null(mc[['tsne_n_neighbors']])) { tsneneighbors <- as.integer(mc$tsne_n_neighbors) } else { tsneneighbors <- as.integer(5) }
^~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:28:42: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['tsne_n_neighbors']])) { tsneneighbors <- as.integer(mc$tsne_n_neighbors) } else { tsneneighbors <- as.integer(5) }
^R/scrubletDoubletDetection.R:28:93: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['tsne_n_neighbors']])) { tsneneighbors <- as.integer(mc$tsne_n_neighbors) } else { tsneneighbors <- as.integer(5) }
^R/scrubletDoubletDetection.R:28:100: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['tsne_n_neighbors']])) { tsneneighbors <- as.integer(mc$tsne_n_neighbors) } else { tsneneighbors <- as.integer(5) }
^R/scrubletDoubletDetection.R:28:133: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['tsne_n_neighbors']])) { tsneneighbors <- as.integer(mc$tsne_n_neighbors) } else { tsneneighbors <- as.integer(5) }
^R/scrubletDoubletDetection.R:29:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['n_iter']])) { niter <- mc$n_iter } else { niter <- 1000 }
^R/scrubletDoubletDetection.R:29:19: style: Only use double-quotes.
if (!is.null(mc[['n_iter']])) { niter <- mc$n_iter } else { niter <- 1000 }
^~~~~~~~R/scrubletDoubletDetection.R:29:32: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['n_iter']])) { niter <- mc$n_iter } else { niter <- 1000 }
^R/scrubletDoubletDetection.R:29:53: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['n_iter']])) { niter <- mc$n_iter } else { niter <- 1000 }
^R/scrubletDoubletDetection.R:29:60: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['n_iter']])) { niter <- mc$n_iter } else { niter <- 1000 }
^R/scrubletDoubletDetection.R:29:76: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['n_iter']])) { niter <- mc$n_iter } else { niter <- 1000 }
^R/scrubletDoubletDetection.R:30:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:30:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^R/scrubletDoubletDetection.R:30:19: style: Only use double-quotes.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:30:43: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^R/scrubletDoubletDetection.R:30:85: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^R/scrubletDoubletDetection.R:30:92: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^R/scrubletDoubletDetection.R:30:113: style: Only use double-quotes.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^~~~~~R/scrubletDoubletDetection.R:30:120: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['umap_order_points']])) { umaporderpoints <- mc$umap_order_points } else { umaporderpoints <- 'True' }
^R/scrubletDoubletDetection.R:31:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:31:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:31:19: style: Only use double-quotes.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:31:43: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:31:85: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:31:92: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:31:113: style: Only use double-quotes.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^~~~~~R/scrubletDoubletDetection.R:31:120: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['tsne_order_points']])) { tsneorderpoints <- mc$tsne_order_points } else { tsneorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:32:1: style: Lines should not be more than 80 characters.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:32:1: style: Use spaces to indent, not tabs.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:32:19: style: Only use double-quotes.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:32:41: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:32:79: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:32:86: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:32:105: style: Only use double-quotes.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^~~~~~R/scrubletDoubletDetection.R:32:112: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if (!is.null(mc[['fa_order_points']])) { faorderpoints <- mc$fa_order_points } else { faorderpoints <- 'True' }
^R/scrubletDoubletDetection.R:33:1: style: Use spaces to indent, not tabs.
^R/scrubletDoubletDetection.R:33:1: style: Trailing whitespace is superfluous.
^R/scrubletDoubletDetection.R:35:1: style: Use spaces to indent, not tabs.
# Install reticulate library if not present.
^R/scrubletDoubletDetection.R:36:1: style: Lines should not be more than 80 characters.
if("reticulate" %in% rownames(installed.packages()) == FALSE) {install.packages("reticulate")}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:36:1: style: Use spaces to indent, not tabs.
if("reticulate" %in% rownames(installed.packages()) == FALSE) {install.packages("reticulate")}
^R/scrubletDoubletDetection.R:36:4: style: Place a space before left parenthesis, except in a function call.
if("reticulate" %in% rownames(installed.packages()) == FALSE) {install.packages("reticulate")}
^R/scrubletDoubletDetection.R:36:64: style: Opening curly braces should never go on their own line and should always be followed by a new line.
if("reticulate" %in% rownames(installed.packages()) == FALSE) {install.packages("reticulate")}
^R/scrubletDoubletDetection.R:36:95: style: Closing curly-braces should always be on their own line, unless it's followed by an else.
if("reticulate" %in% rownames(installed.packages()) == FALSE) {install.packages("reticulate")}
^R/scrubletDoubletDetection.R:37:1: style: Use spaces to indent, not tabs.
library(reticulate)
^R/scrubletDoubletDetection.R:38:1: style: Use spaces to indent, not tabs.
^R/scrubletDoubletDetection.R:38:1: style: Trailing whitespace is superfluous.
^R/scrubletDoubletDetection.R:39:1: style: Lines should not be more than 80 characters.
# check if required python packages in appropriate virtual env already exists. Create one if it doesn't
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:39:1: style: Use spaces to indent, not tabs.
# check if required python packages in appropriate virtual env already exists. Create one if it doesn't
^R/scrubletDoubletDetection.R:39:105: style: Trailing whitespace is superfluous.
# check if required python packages in appropriate virtual env already exists. Create one if it doesn't
^R/scrubletDoubletDetection.R:40:1: style: Use spaces to indent, not tabs.
all_venvs <- virtualenv_list()
^R/scrubletDoubletDetection.R:41:1: style: Use spaces to indent, not tabs.
if (grepl(pattern="r-scrubletvenv",x=all_venvs)==FALSE){
^R/scrubletDoubletDetection.R:41:19: style: Put spaces around all infix operators.
if (grepl(pattern="r-scrubletvenv",x=all_venvs)==FALSE){
~^~R/scrubletDoubletDetection.R:41:37: style: Commas should always have a space after.
if (grepl(pattern="r-scrubletvenv",x=all_venvs)==FALSE){
^R/scrubletDoubletDetection.R:41:38: style: Put spaces around all infix operators.
if (grepl(pattern="r-scrubletvenv",x=all_venvs)==FALSE){
~^~R/scrubletDoubletDetection.R:41:49: style: Put spaces around all infix operators.
if (grepl(pattern="r-scrubletvenv",x=all_venvs)==FALSE){
~^~~R/scrubletDoubletDetection.R:41:56: style: There should be a space between right parenthesis and an opening curly brace.
if (grepl(pattern="r-scrubletvenv",x=all_venvs)==FALSE){
^~R/scrubletDoubletDetection.R:42:1: style: Use spaces to indent, not tabs.
virtualenv_create("r-scrubletvenv")
^~R/scrubletDoubletDetection.R:43:1: style: Use spaces to indent, not tabs.
virtualenv_install("r-scrubletvenv", "scipy")
^~R/scrubletDoubletDetection.R:44:1: style: Use spaces to indent, not tabs.
virtualenv_install("r-scrubletvenv", "scrublet")
^~R/scrubletDoubletDetection.R:45:1: style: Use spaces to indent, not tabs.
virtualenv_install("r-scrubletvenv", "matplotlib")
^~R/scrubletDoubletDetection.R:46:1: style: Use spaces to indent, not tabs.
}
^R/scrubletDoubletDetection.R:47:1: style: Use spaces to indent, not tabs.
^R/scrubletDoubletDetection.R:47:1: style: Trailing whitespace is superfluous.
^R/scrubletDoubletDetection.R:48:1: style: Use spaces to indent, not tabs.
# Load virtual env and python script
^R/scrubletDoubletDetection.R:49:1: style: Use spaces to indent, not tabs.
reticulate::use_virtualenv("r-scrubletvenv")
^R/scrubletDoubletDetection.R:50:1: style: Use spaces to indent, not tabs.
reticulate::source_python("scrublet_test.py")
^R/scrubletDoubletDetection.R:51:1: style: Use spaces to indent, not tabs.
^R/scrubletDoubletDetection.R:51:1: style: Trailing whitespace is superfluous.
^R/scrubletDoubletDetection.R:52:1: style: Use spaces to indent, not tabs.
# call python scrublet function and write detected doublet scores to file
^R/scrubletDoubletDetection.R:53:1: style: Use spaces to indent, not tabs.
^R/scrubletDoubletDetection.R:53:1: style: Trailing whitespace is superfluous.
^R/scrubletDoubletDetection.R:54:1: style: Lines should not be more than 80 characters.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:54:1: style: Use spaces to indent, not tabs.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
^R/scrubletDoubletDetection.R:54:63: style: Commas should always have a space after.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
^R/scrubletDoubletDetection.R:54:69: style: Commas should always have a space after.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
^R/scrubletDoubletDetection.R:54:76: style: Commas should always have a space after.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
^R/scrubletDoubletDetection.R:54:97: style: Put spaces around all infix operators.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
~^~R/scrubletDoubletDetection.R:54:102: style: Commas should always have a space after.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
^R/scrubletDoubletDetection.R:54:112: style: Put spaces around all infix operators.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
~^~R/scrubletDoubletDetection.R:54:123: style: Commas should always have a space after.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
^R/scrubletDoubletDetection.R:54:132: style: Put spaces around all infix operators.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
~^~R/scrubletDoubletDetection.R:54:168: style: Put spaces around all infix operators.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
~^~R/scrubletDoubletDetection.R:54:197: style: Put spaces around all infix operators.
doubletscore <- py_capture_output(run_Scrublet(counts_matrix,genes,output,expected_doublet_rate=edr,min_counts=mincounts,min_cells=mincells, min_gene_variability_pctl=mingenevarpctl, n_prin_comps=nprincomps,
~^~R/scrubletDoubletDetection.R:55:1: style: Lines should not be more than 80 characters.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R/scrubletDoubletDetection.R:55:1: style: Use spaces to indent, not tabs.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
^R/scrubletDoubletDetection.R:55:18: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:55:42: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:55:57: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:55:79: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:55:101: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:55:126: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:55:161: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:55:194: style: Put spaces around all infix operators.
umap_n_neighbors=umapneighbors, min_dist=mindist, angle=ang, tsne_n_neighbors=tsneneighbors, n_iter=niter, umap_order_points=umaporderpoints, tsne_order_points=tsneorderpoints, fa_order_points=faorderpoints),
~^~R/scrubletDoubletDetection.R:56:1: style: Use spaces to indent, not tabs.
type = c("stderr","stdout"))
^R/scrubletDoubletDetection.R:56:21: style: Commas should always have a space after.
type = c("stderr","stdout"))
^R/scrubletDoubletDetection.R:57:1: style: Use spaces to indent, not tabs.
^
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