diff --git a/NAMESPACE b/NAMESPACE index ed96b58..fd8685a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,5 +1,6 @@ # Generated by roxygen2: do not edit by hand +S3method(drop.levels,Seurat) S3method(plot,GeneExpHist) S3method(plot,Metadata.Cor.Heatmap) S3method(plot,Metadata.categ.pie) @@ -70,7 +71,6 @@ export(check.genes) export(clUMAP) export(clip10Xcellname) export(create.metadata.vector) -export(drop.levels.Seurat) export(find_prefix_in_cell_IDs) export(fix.orig.ident) export(fixZeroIndexing.seurat) diff --git a/R/Seurat.Utils.Metadata.R b/R/Seurat.Utils.Metadata.R index 1150681..a126e11 100644 --- a/R/Seurat.Utils.Metadata.R +++ b/R/Seurat.Utils.Metadata.R @@ -694,7 +694,7 @@ plot.Metadata.categ.pie <- function(metacol = 'Singlet.status' , obj = combined.obj, max.categs = 20, both_pc_and_value = T, ...) { categ_pivot <- table(obj[[metacol]]) stopifnot(length(categ_pivot) < max.categs) - qpie(categ_pivot, plotname = plot_name + qpie(categ_pivot, plotname = FixPlotName(make.names(plot_name)) , both_pc_and_value = both_pc_and_value , LegendSide = F, labels = NULL, LegendTitle = '', ...) } diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R index c77573f..416450b 100644 --- a/R/Seurat.Utils.R +++ b/R/Seurat.Utils.R @@ -3,6 +3,7 @@ # ____________________________________________________________________ # devtools::load_all(path = '~/GitHub/Packages/Seurat.utils'); # source("~/GitHub/Packages/Seurat.utils/R/Seurat.Utils.R") +# source("~/GitHub/Packages/Seurat.utils/R/Seurat.Utils.Metadata.R") # _________________________________________________________________________________________________ # Cluster.Auto-naming.DE.R @@ -12,7 +13,7 @@ # _________________________________________________________________________________________________ # require(princurve) # only for AutoNumber.by.PrinCurve -backup + # _________________________________________________________________________________________________ # General ______________________________ ---- @@ -543,7 +544,7 @@ Percent.in.Trome <- function(obj = combined.obj, n.genes.barplot = 25 #' @export gene.expression.level.plots <- function(gene = 'TOP2A', obj = ls.Seurat[[1]] , slot = c('counts', 'data')[2] - , w = 7, h = 4 + , w = 9, h = 4 , ... ) { print(gene) if (gene %in% rownames(obj)) { diff --git a/man/LoadAllSeurats.Rd b/man/LoadAllSeurats.Rd index bcc9ac0..b326fc7 100644 --- a/man/LoadAllSeurats.Rd +++ b/man/LoadAllSeurats.Rd @@ -8,7 +8,9 @@ LoadAllSeurats( InputDir, file.pattern = "^filtered.+Rds$", string.remove1 = c(F, "filtered_feature_bc_matrix.", "raw_feature_bc_matrix.")[2], - string.remove2 = c(F, ".min.cells.10.min.features.200.Rds")[2] + string.remove2 = c(F, ".min.cells.10.min.features.200.Rds")[2], + string.replace1 = "", + string.replace2 = "" ) } \arguments{ @@ -19,6 +21,10 @@ LoadAllSeurats( \item{string.remove1}{A character string or FALSE. If a string is provided, it is removed from file names. Default is "filtered_feature_bc_matrix.".} \item{string.remove2}{A character string or FALSE. If a string is provided, it is removed from file names. Default is ".min.cells.10.min.features.200.Rds".} + +\item{string.replace1}{Replacement "string.remove1" to this string. Default is "".} + +\item{string.replace2}{Replacement "string.remove1" to this string. Default is "".} } \description{ This function loads all Seurat objects found in a directory. It also works with symbolic links (but not with aliases). diff --git a/man/drop.levels.Seurat.Rd b/man/drop.levels.Seurat.Rd index f3b7e85..c575bd1 100644 --- a/man/drop.levels.Seurat.Rd +++ b/man/drop.levels.Seurat.Rd @@ -4,7 +4,7 @@ \alias{drop.levels.Seurat} \title{drop.levels.Seurat} \usage{ -drop.levels.Seurat(obj = combined.obj, verbose = TRUE) +\method{drop.levels}{Seurat}(obj = combined.obj, verbose = TRUE) } \arguments{ \item{obj}{A Seurat object.} diff --git a/man/gene.expression.level.plots.Rd b/man/gene.expression.level.plots.Rd index a274807..344a15b 100644 --- a/man/gene.expression.level.plots.Rd +++ b/man/gene.expression.level.plots.Rd @@ -8,6 +8,8 @@ gene.expression.level.plots( gene = "TOP2A", obj = ls.Seurat[[1]], slot = c("counts", "data")[2], + w = 7, + h = 4, ... ) } diff --git a/man/isave.RDS.Rd b/man/isave.RDS.Rd index f8f42fb..8d583c5 100644 --- a/man/isave.RDS.Rd +++ b/man/isave.RDS.Rd @@ -16,7 +16,7 @@ isave.RDS( "/users/abel.vertesy/", showMemObject = T, saveParams = T, - compress = TRUE, + compress = FALSE, test_read = FALSE ) } diff --git a/man/multiFeaturePlot.A4.Rd b/man/multiFeaturePlot.A4.Rd index a08e0ed..2d33bd7 100644 --- a/man/multiFeaturePlot.A4.Rd +++ b/man/multiFeaturePlot.A4.Rd @@ -27,9 +27,7 @@ multiFeaturePlot.A4( h = hA4, scaling = 1, format = c("jpg", "pdf", "png")[1], - solo = MarkdownHelpers::FALSE.unless("b.solo.plot"), raster = MarkdownHelpers::FALSE.unless("b.raster"), - raster.dpi = c(512, 512)/4, ... ) }