From 31de8d59c1c763eb35f7e38d72941a0d5829bb86 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Thu, 11 Apr 2024 12:42:30 -0400
Subject: [PATCH] chore: run document

---
 R/vis_spatial_in_situ.R         | 13 +++++++------
 man/addGiottoImageToSpatPlot.Rd |  2 +-
 man/spatInSituPlotDensity.Rd    |  2 +-
 man/spatInSituPlotHex.Rd        |  4 ++--
 man/spatInSituPlotPoints.Rd     |  3 ++-
 5 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/R/vis_spatial_in_situ.R b/R/vis_spatial_in_situ.R
index f0bbb56..f85029d 100644
--- a/R/vis_spatial_in_situ.R
+++ b/R/vis_spatial_in_situ.R
@@ -22,7 +22,8 @@
 #' @param expand_counts expand feature coordinate counts (see details)
 #' @param count_info_column column name with count information
 #' (if expand_counts = TRUE)
-#' @param jitter maximum x,y jitter provided as c(x, y)
+#' @param jitter numeric. Maximum x,y jitter provided as c(x, y) or a single
+#' number which will be recycled to length 2.
 #' @param axis_text axis text size
 #' @param axis_title title text size
 #' @param legend_text legend text size
@@ -563,8 +564,8 @@ spatInSituPlotPoints <- function(gobject,
 #' @family In Situ visualizations
 #' @returns ggplot
 #' @examples
-#' g <- GiottoData::loadGiottoMini("vizgen") 
-#' spatInSituPlotHex(g, feats = c("Mlc1", "Gprc5b", "Gfap"), 
+#' g <- GiottoData::loadGiottoMini("vizgen")
+#' spatInSituPlotHex(g, feats = c("Mlc1", "Gprc5b", "Gfap"),
 #' polygon_feat_type = "z0")
 #' @export
 spatInSituPlotHex <- function(
@@ -850,9 +851,9 @@ spatInSituPlotHex <- function(
 #' @returns ggplot
 #' @examples
 #' g <- GiottoData::loadGiottoMini("vizgen")
-#' spatInSituPlotDensity(g, feats = c("Mlc1", "Gprc5b", "Gfap"), 
+#' spatInSituPlotDensity(g, feats = c("Mlc1", "Gprc5b", "Gfap"),
 #' polygon_feat_type = "z0")
-#' 
+#'
 #' @export
 spatInSituPlotDensity <- function(
         gobject,
@@ -1014,7 +1015,7 @@ spatInSituPlotDensity <- function(
 #' g <- GiottoData::loadGiottoMini("vizgen")
 #' x <- GiottoClass::getFeatureInfo(g)
 #' x <- data.table::as.data.table(x)
-#' 
+#'
 #' @keywords internal
 #' @export
 expand_feature_info <- function(
diff --git a/man/addGiottoImageToSpatPlot.Rd b/man/addGiottoImageToSpatPlot.Rd
index c5da653..3dcaa61 100644
--- a/man/addGiottoImageToSpatPlot.Rd
+++ b/man/addGiottoImageToSpatPlot.Rd
@@ -32,7 +32,7 @@ Add a giotto image to a spatial ggplot object post creation
 \examples{
 g <- GiottoData::loadGiottoMini("visium")
 
-my_giottoimage <- GiottoClass::createGiottoImage(g, 
+my_giottoimage <- GiottoClass::createGiottoImage(g,
 mg_object = system.file("image.png", package = "GiottoVisuals"),
 name = 'image')
 
diff --git a/man/spatInSituPlotDensity.Rd b/man/spatInSituPlotDensity.Rd
index 3403671..9ddab41 100644
--- a/man/spatInSituPlotDensity.Rd
+++ b/man/spatInSituPlotDensity.Rd
@@ -107,7 +107,7 @@ TODO
 }
 \examples{
 g <- GiottoData::loadGiottoMini("vizgen")
-spatInSituPlotDensity(g, feats = c("Mlc1", "Gprc5b", "Gfap"), 
+spatInSituPlotDensity(g, feats = c("Mlc1", "Gprc5b", "Gfap"),
 polygon_feat_type = "z0")
 
 }
diff --git a/man/spatInSituPlotHex.Rd b/man/spatInSituPlotHex.Rd
index 364ea8b..8037180 100644
--- a/man/spatInSituPlotHex.Rd
+++ b/man/spatInSituPlotHex.Rd
@@ -114,8 +114,8 @@ modalities at the spatial in situ level
 TODO
 }
 \examples{
-g <- GiottoData::loadGiottoMini("vizgen") 
-spatInSituPlotHex(g, feats = c("Mlc1", "Gprc5b", "Gfap"), 
+g <- GiottoData::loadGiottoMini("vizgen")
+spatInSituPlotHex(g, feats = c("Mlc1", "Gprc5b", "Gfap"),
 polygon_feat_type = "z0")
 }
 \seealso{
diff --git a/man/spatInSituPlotPoints.Rd b/man/spatInSituPlotPoints.Rd
index a061e1c..1e8afd1 100644
--- a/man/spatInSituPlotPoints.Rd
+++ b/man/spatInSituPlotPoints.Rd
@@ -93,7 +93,8 @@ to include}
 \item{count_info_column}{column name with count information
 (if expand_counts = TRUE)}
 
-\item{jitter}{maximum x,y jitter provided as c(x, y)}
+\item{jitter}{numeric. Maximum x,y jitter provided as c(x, y) or a single
+number which will be recycled to length 2.}
 
 \item{show_polygon}{overlay polygon information (e.g. cell shape)}