diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R index 88debe1..2d4343f 100644 --- a/R/Seurat.Utils.R +++ b/R/Seurat.Utils.R @@ -3098,7 +3098,7 @@ multiFeaturePlot.A4 <- function(list.of.genes # Save multiple FeaturePlots, as j , w = wA4, h = hA4, scaling = 1 , format = c('jpg', 'pdf', 'png')[1] , raster = MarkdownHelpers::FALSE.unless('b.raster') - # , raster.dpi = c(512, 512)/4 + , raster.dpi = NULL , ... # , jpeg.res = 225, jpeg.q = 90 ) { @@ -3125,14 +3125,13 @@ multiFeaturePlot.A4 <- function(list.of.genes # Save multiple FeaturePlots, as j genes = list.of.genes.found[lsG[[i]]] iprint(i,genes ) plotname = kpp(c(prefix, plot.reduction,i, genes, suffix, format )) - - if (raster == TRUE) cex <- 1 # https://github.com/satijalab/seurat/issues/7466#issuecomment-1601276032 + if (raster == TRUE) cex <- 1 # https://github.com/satijalab/seurat/issues/7466#issuecomment-1601276032 "Remove in 2024, fixed in 4.4.0" plot.list = Seurat::FeaturePlot(object = obj, features = genes, reduction = plot.reduction, combine = F , ncol = nr.Col, cols = colors , min.cutoff = gene.min.exp, max.cutoff = gene.max.exp , raster = raster - # , raster.dpi = raster.dpi + , raster.dpi = raster.dpi , pt.size = cex , ...) @@ -3338,7 +3337,8 @@ qQC.plots.BrainOrg <- function(obj = combined.obj, title = "Top 4 QC markers on #' } #' } #' @export -qMarkerCheck.BrainOrg <- function(obj = combined.obj, custom.genes = F, suffix = "") { +qMarkerCheck.BrainOrg <- function(obj = combined.obj, custom.genes = F, suffix = "" + , raster.dpi = c(512, 256) / 2) { Signature.Genes.Top24 <- if (!isFALSE(custom.genes)) custom.genes else { Signature.Genes.Top24 <- c( @@ -3364,7 +3364,8 @@ qMarkerCheck.BrainOrg <- function(obj = combined.obj, custom.genes = F, suffix = multiFeaturePlot.A4(obj = obj, layout = "tall" , list.of.genes = Signature.Genes.Top24 , caption = names(Signature.Genes.Top24) - , foldername = sppp('Signature.Genes.Top24', suffix)) + , foldername = sppp('Signature.Genes.Top24', suffix) + , raster.dpi = raster.dpi) }