From f8836f52a9ed1f02d8822c106695b4d1357c614c Mon Sep 17 00:00:00 2001 From: Joseph Tumulty <141662454+JTumulty@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:47:03 -0400 Subject: [PATCH 1/6] Update plotMetrics.R Rename columns before plotting --- R/plotMetrics.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/R/plotMetrics.R b/R/plotMetrics.R index 6cb0dbf..a9b0b19 100644 --- a/R/plotMetrics.R +++ b/R/plotMetrics.R @@ -43,6 +43,9 @@ plotMetrics <- function(sce, detected = "detected", palette = "#33ADFF") { metrics <- as.data.frame(colData(sce)) + colnames(metrics)[colnames(metrics)==detected] <- "detected" + colnames(metrics)[colnames(metrics)==subsets_mito_percent] <- "subsets_mito_percent" + p <- ggplot(metrics, aes(x = detected, y = subsets_mito_percent)) + labs(x = "Unique genes found", y = "Percent reads mitochondrial") + geom_point(colour = palette) From c24f096ea3b585acd2226c671e5ee48bd398292e Mon Sep 17 00:00:00 2001 From: Joseph Tumulty <141662454+JTumulty@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:49:43 -0400 Subject: [PATCH 2/6] Update plotFiltering.R Rename provided columns before plotting --- R/plotFiltering.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/plotFiltering.R b/R/plotFiltering.R index 000b5c1..9a959d0 100644 --- a/R/plotFiltering.R +++ b/R/plotFiltering.R @@ -65,7 +65,9 @@ plotFiltering <- function(sce, model = NULL, posterior_cutoff = 0.75, detected = "detected", subsets_mito_percent = "subsets_mito_percent") { metrics <- as.data.frame(colData(sce)) - + colnames(metrics)[colnames(metrics)==detected] <- "detected" + colnames(metrics)[colnames(metrics)==subsets_mito_percent] <- "subsets_mito_percent" + if (is.null(model)) { warning("call 'mixtureModel' explicitly to get stable model features") model <- mixtureModel(sce) From 3f08640d65e849e66d75d9708f666751d1b72dd0 Mon Sep 17 00:00:00 2001 From: Joseph Tumulty <141662454+JTumulty@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:50:38 -0400 Subject: [PATCH 3/6] Update plotModel.R Rename provided columns before plotting --- R/plotModel.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/plotModel.R b/R/plotModel.R index 8590e70..a3e33b0 100644 --- a/R/plotModel.R +++ b/R/plotModel.R @@ -43,6 +43,8 @@ plotModel <- function(sce, model = NULL, detected = "detected", subsets_mito_percent = "subsets_mito_percent") { metrics <- as.data.frame(colData(sce)) + colnames(metrics)[colnames(metrics)==detected] <- "detected" + colnames(metrics)[colnames(metrics)==subsets_mito_percent] <- "subsets_mito_percent" if (is.null(model)) { warning("call 'mixtureModel' explicitly to get stable model features") From d6c5025251ec561a89b4efade76a9ff0b77408c3 Mon Sep 17 00:00:00 2001 From: Joseph Tumulty <141662454+JTumulty@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:52:01 -0400 Subject: [PATCH 4/6] Update mixtureModel.R Rename provided columns before fitting model --- R/mixtureModel.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/mixtureModel.R b/R/mixtureModel.R index 426ba65..c3a3f37 100644 --- a/R/mixtureModel.R +++ b/R/mixtureModel.R @@ -47,6 +47,8 @@ mixtureModel <- function(sce, model_type = "linear", detected = "detected", subsets_mito_percent = "subsets_mito_percent") { metrics <- as.data.frame(colData(sce)) + colnames(metrics)[colnames(metrics)==detected] <- "detected" + colnames(metrics)[colnames(metrics)==subsets_mito_percent] <- "subsets_mito_percent" if (model_type == "linear") { model <- flexmix(subsets_mito_percent~detected, From 98dcf09c9e3ec00eff90dbbcbc1dc212fc68f889 Mon Sep 17 00:00:00 2001 From: Joseph Tumulty <141662454+JTumulty@users.noreply.github.com> Date: Thu, 10 Oct 2024 16:55:48 -0400 Subject: [PATCH 5/6] Update get1DCutoff.R Rename provided column --- R/get1DCutoff.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/get1DCutoff.R b/R/get1DCutoff.R index 475c4b0..945441b 100644 --- a/R/get1DCutoff.R +++ b/R/get1DCutoff.R @@ -44,6 +44,7 @@ get1DCutoff <- function(sce, model = NULL, posterior_cutoff = 0.75, subsets_mito_percent = "subsets_mito_percent") { metrics <- as.data.frame(colData(sce)) + colnames(metrics)[colnames(metrics)==subsets_mito_percent] <- "subsets_mito_percent" if (is.null(model)) { warning("call 'mixtureModel' explicitly to get stable model features") From e2d325c2afe2aa2ee95899963baf8e669487a6ce Mon Sep 17 00:00:00 2001 From: Joseph Tumulty <141662454+JTumulty@users.noreply.github.com> Date: Thu, 10 Oct 2024 17:01:00 -0400 Subject: [PATCH 6/6] Update filterCells.R Add parameters "detected=" and "subsets_mito_percent=" to function and rename columns in data frame based on provided value. Also updated list of parameters to include these --- R/filterCells.R | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/R/filterCells.R b/R/filterCells.R index ba3bcc7..fbd0d1b 100644 --- a/R/filterCells.R +++ b/R/filterCells.R @@ -26,6 +26,15 @@ #' than it are kept. #' Default = TRUE #' +#' @param detected (character) Column name in sce giving the number of unique +#' genes detected per cell. This name is inherited by default from scater's +#' addPerCellQC() function. +#' +#' @param subsets_mito_percent (character) Column name in sce giving the +#' percent of reads mapping to mitochondrial genes. This name is inherited +#' from scater's addPerCellQC() function, provided the subset "mito" with +#' names of all mitochondrial genes is passed in. See examples for details. +#' #' @param verbose (boolean) Whether to report how many cells (columns) are being #' removed from the SingleCellExperiment object. #' Default = TRUE @@ -53,9 +62,13 @@ filterCells <- function(sce, model = NULL, posterior_cutoff = 0.75, keep_all_below_boundary = TRUE, - enforce_left_cutoff = TRUE, verbose = TRUE) { + enforce_left_cutoff = TRUE, + detected = "detected", subsets_mito_percent = "subsets_mito_percent", + verbose = TRUE) { metrics <- as.data.frame(colData(sce)) - + colnames(metrics)[colnames(metrics)==detected] <- "detected" + colnames(metrics)[colnames(metrics)==subsets_mito_percent] <- "subsets_mito_percent" + if (is.null(model)) { warning("call 'mixtureModel' explicitly to get stable model features") model <- mixtureModel(sce)