minor changes (48a9fb1d) · Commits · github_fork / DAseq2

R/SeuratMarkerFinder.R

+4 −0

Original line number	Diff line number	Diff line
		@@ -32,6 +32,8 @@ SeuratMarkerFinder <- function(
		output.markers[[as.character(ii)]] <- FindMarkers(
		object, ident.1 = ii, ...
		)
		output.markers[[as.character(ii)]]$pct.diff <- output.markers[[as.character(ii)]]$pct.1 -
		output.markers[[as.character(ii)]]$pct.2
		}
		}

		@@ -101,6 +103,8 @@ SeuratLocalMarkers <- function(
		output.markers <- FindMarkers(
		object, ident.1 = "da", ident.2 = "local", ...
		)
		output.markers[[as.character(ii)]]$pct.diff <- output.markers[[as.character(ii)]]$pct.1 -
		output.markers[[as.character(ii)]]$pct.2
		}
		return(output.markers)
		}

R/getDAregion.R

+3 −2

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@
		#' @param do.plot a logical value to indicate whether to return ggplot objects showing the results, default True
		#' @param plot.embedding size N-by-2 matrix, 2D embedding for the cells
		#' @param size cell size to use in the plot, default 0.5
		#' @param do.label a logical value to indicate whether to label each DA region with text, default False

		#' @param ... other parameters to pass to Seurat FindClusters()
		#'
		@@ -35,7 +36,7 @@ getDAregion <- function(
		X, da.cells,
		cell.labels, labels.1, labels.2,
		prune.SNN = 1/15, resolution = 0.05, group.singletons = F, min.cell = 15,
		do.plot = T, plot.embedding = NULL, size = 0.5,
		do.plot = T, plot.embedding = NULL, size = 0.5, do.label = F,
		...
		){
		if(!inherits(x = X, what = "matrix")){
		@@ -140,7 +141,7 @@ getDAregion <- function(
		X.da.order <- order(X.da.label, decreasing = F)
		X.region.plot <- plotCellLabel(
		X = plot.embedding[X.da.order,], label = as.factor(X.da.label[X.da.order]),
		size = size, do.label = F
		size = size, do.label = do.label, label.plot = as.character(c(1:X.n.da))
		) + scale_color_manual(values = c("gray",hue_pal()(X.n.da)), breaks = c(1:X.n.da))
		} else {
		X.region.plot <- NULL

docs/reference/getDAregion.html

+5 −1

Original line number	Diff line number	Diff line
		@@ -131,7 +131,7 @@ coherent DA regions.</p>
		<pre class="usage"><span class='fu'>getDAregion</span>(<span class='no'>X</span>, <span class='no'>da.cells</span>, <span class='no'>cell.labels</span>, <span class='no'>labels.1</span>, <span class='no'>labels.2</span>,
		<span class='kw'>prune.SNN</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>15</span>, <span class='kw'>resolution</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>group.singletons</span> <span class='kw'>=</span> <span class='no'>F</span>,
		<span class='kw'>min.cell</span> <span class='kw'>=</span> <span class='fl'>15</span>, <span class='kw'>do.plot</span> <span class='kw'>=</span> <span class='no'>T</span>, <span class='kw'>plot.embedding</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
		<span class='no'>...</span>)</pre>
		<span class='kw'>do.label</span> <span class='kw'>=</span> <span class='no'>F</span>, <span class='no'>...</span>)</pre>

		<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
		<table class="ref-arguments">
		@@ -184,6 +184,10 @@ coherent DA regions.</p>
		<th>size</th>
		<td><p>cell size to use in the plot, default 0.5</p></td>
		</tr>
		<tr>
		<th>do.label</th>
		<td><p>a logical value to indicate whether to label each DA region with text, default False</p></td>
		</tr>
		<tr>
		<th>...</th>
		<td><p>other parameters to pass to Seurat FindClusters()</p></td>

man/getDAregion.Rd

+3 −1

Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@
		getDAregion(X, da.cells, cell.labels, labels.1, labels.2,
		prune.SNN = 1/15, resolution = 0.05, group.singletons = F,
		min.cell = 15, do.plot = T, plot.embedding = NULL, size = 0.5,
		...)
		do.label = F, ...)
		}
		\arguments{
		\item{X}{size N-by-p matrix, input merged dataset of interest after dimension reduction}
		@@ -34,6 +34,8 @@ getDAregion(X, da.cells, cell.labels, labels.1, labels.2,

		\item{size}{cell size to use in the plot, default 0.5}

		\item{do.label}{a logical value to indicate whether to label each DA region with text, default False}

		\item{...}{other parameters to pass to Seurat FindClusters()}
		}
		\value{

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