diff --git a/R/add_key.R b/R/add_key.R
index 648ecc30..ce851b66 100644
--- a/R/add_key.R
+++ b/R/add_key.R
@@ -21,13 +21,20 @@
 #'     head(spe$key)
 #'
 #'     ## We can clean it
+#'     spe$key_original <- spe$key
 #'     spe$key <- NULL
 #'
 #'     ## and then add it back
-#'     head(add_key(spe)$key)
+#'     spe <- add_key(spe)
+#'     head(spe$key)
 #'
 #'     ## Note that the original 'key' order was 'sample_id'_'barcode' and we'
 #'     ## have since changed it to 'barcode'_'sample_id'.
+#'
+#'     ## Below we restore the original 'key'
+#'     spe$key <- spe$key_original
+#'     spe$key_original <- NULL
+#'     head(spe$key)
 #' }
 add_key <- function(spe, overwrite = TRUE) {
     if ("key" %in% colnames(colData(spe))) {
diff --git a/R/add_qc_metrics.R b/R/add_qc_metrics.R
index c1213184..a5c7ca32 100644
--- a/R/add_qc_metrics.R
+++ b/R/add_qc_metrics.R
@@ -90,7 +90,7 @@
 #' vis_clus(spe_qc, sample_id = "Br6432_ant", clustervar = "our_low_lib_edge")
 #'
 #' ## Clean up
-#' rm(spe_qc, spec_pre_qc)
+#' rm(spe_qc, spe_pre_qc, vars)
 #'
 add_qc_metrics <- function(spe, overwrite = FALSE) {
     stopifnot("in_tissue" %in% colnames(colData(spe)))
diff --git a/R/check_sce_layer.R b/R/check_sce_layer.R
index e7280113..5ca9b5ae 100644
--- a/R/check_sce_layer.R
+++ b/R/check_sce_layer.R
@@ -14,10 +14,11 @@
 #'
 #' @examples
 #'
-#' ## Obtain the necessary data
+#' ## Obtain example data from the HumanPilot project
+#' ## (Maynard, Collado-Torres, et al, 2021)
 #' if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
 #'
-#' ## Check the object
+#' ## Check the pseudo-bulked data
 #' check_sce_layer(sce_layer)
 check_sce_layer <- function(sce_layer, variables = "spatialLIBD") {
     ## Should be a SingleCellExperiment object
diff --git a/R/vis_clus.R b/R/vis_clus.R
index 1bca16bf..e1e0eaa0 100644
--- a/R/vis_clus.R
+++ b/R/vis_clus.R
@@ -4,7 +4,11 @@
 #' using (by default) the histology information on the background. To visualize
 #' gene-level (or any continuous variable) use [vis_gene()].
 #'
-#' @inheritParams run_app
+#' @param spe A
+#' [SpatialExperiment-class][SpatialExperiment::SpatialExperiment-class]
+#' object. See [fetch_data()] for how to download some example objects or
+#' [read10xVisiumWrapper()] to read in `spaceranger --count` output files and
+#' build your own `spe` object.
 #' @param sampleid A `character(1)` specifying which sample to plot from
 #' `colData(spe)$sample_id` (formerly `colData(spe)$sample_name`).
 #' @param clustervar A `character(1)` with the name of the `colData(spe)`
diff --git a/R/vis_clus_p.R b/R/vis_clus_p.R
index d2b37cec..f74b95f6 100644
--- a/R/vis_clus_p.R
+++ b/R/vis_clus_p.R
@@ -6,8 +6,8 @@
 #' gene-level (or any continuous variable) use [vis_gene_p()].
 #'
 #' @inheritParams vis_clus
-#' @param d A data.frame with the sample-level information. This is typically
-#' obtained using `cbind(colData(spe), spatialCoords(spe))`.
+#' @param d A `data.frame()` with the sample-level information. This is
+#' typically obtained using `cbind(colData(spe), spatialCoords(spe))`.
 #' @param title The title for the plot.
 #'
 #' @return A [ggplot2][ggplot2::ggplot] object.
diff --git a/R/vis_gene.R b/R/vis_gene.R
index 38a233aa..ed056ba5 100644
--- a/R/vis_gene.R
+++ b/R/vis_gene.R
@@ -7,11 +7,11 @@
 #'
 #' @inheritParams vis_clus
 #' @param geneid A `character()` specifying the gene ID(s) stored in
-#' `rowData(spe)$gene_search` or a continuous variable(s) stored in `colData(spe)`
-#' to visualize. For each ID, if `rowData(spe)$gene_search` is missing, then
-#' `rownames(spe)` is used to search for the gene ID. When a vector of length > 1
-#' is supplied, the continuous variables are combined according to \code{multi_gene_method},
-#' producing a single value for each spot.
+#' `rowData(spe)$gene_search` or a continuous variable(s) stored in
+#' `colData(spe)` to visualize. For each ID, if `rowData(spe)$gene_search` is
+#' missing, then `rownames(spe)` is used to search for the gene ID. When a
+#' vector of length > 1 is supplied, the continuous variables are combined
+#' according to `multi_gene_method`, producing a single value for each spot.
 #' @param assayname The name of the `assays(spe)` to use for extracting the
 #' gene expression data. Defaults to `logcounts`.
 #' @param minCount A `numeric(1)` specifying the minimum gene expression (or
@@ -25,9 +25,9 @@
 #' dependent on cell density.
 #' @param cont_colors A `character()` vector of colors that supersedes the
 #' `viridis` argument.
-#' @param multi_gene_method A \code{character(1)}: either "pca", "sparsity", or
-#' "z_score". This parameter controls how multiple continuous variables are
-#' combined for visualization, and only applies when \code{geneid} has length
+#' @param multi_gene_method A `character(1)`: either `"pca"`, `"sparsity"`, or
+#' `"z_score"`. This parameter controls how multiple continuous variables are
+#' combined for visualization, and only applies when `geneid` has length
 #' great than 1. `z_score`: to summarize multiple continuous variables, each is
 #' normalized to represent a Z-score. The multiple scores are then averaged.
 #' `pca`: PCA dimension reduction is conducted on the matrix formed by the
diff --git a/R/vis_gene_p.R b/R/vis_gene_p.R
index 632b864c..baeee29e 100644
--- a/R/vis_gene_p.R
+++ b/R/vis_gene_p.R
@@ -3,12 +3,12 @@
 #' This function visualizes the gene expression stored in `assays(spe)` or any
 #' continuous variable stored in `colData(spe)` for one given sample at the
 #' spot-level using (by default) the histology information on the background.
-#' This is the function that does all the plotting behind [vis_gene()].
+#' This is the function that does all the plotting behind [vis_gene()]
 #' To visualize clusters (or any discrete variable) use [vis_clus_p()].
 #'
-#' @param d A data.frame with the sample-level information. This is typically
-#' obtained using `cbind(colData(spe), spatialCoords(spe))`.
-#' The data.frame has to contain
+#' @param d A `data.frame()` with the sample-level information. This is
+#' typically obtained using `cbind(colData(spe), spatialCoords(spe))`.
+#' The `data.frame` has to contain
 #' a column with the continuous variable data to plot stored under `d$COUNT`.
 #' @param legend_title A `character(1)` specifying the legend title.
 #' @inheritParams vis_clus_p
diff --git a/man/add_images.Rd b/man/add_images.Rd
index dfe964fd..6e85ffb5 100644
--- a/man/add_images.Rd
+++ b/man/add_images.Rd
@@ -14,11 +14,11 @@ add_images(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{image_dir}{A \code{character(1)} specifying a path to a directory containing
 image files with the pattern \code{sampleID_pattern.png}.}
diff --git a/man/add_key.Rd b/man/add_key.Rd
index 699aaf67..b13e780f 100644
--- a/man/add_key.Rd
+++ b/man/add_key.Rd
@@ -31,12 +31,19 @@ if (enough_ram()) {
     head(spe$key)
 
     ## We can clean it
+    spe$key_original <- spe$key
     spe$key <- NULL
 
     ## and then add it back
-    head(add_key(spe)$key)
+    spe <- add_key(spe)
+    head(spe$key)
 
     ## Note that the original 'key' order was 'sample_id'_'barcode' and we'
     ## have since changed it to 'barcode'_'sample_id'.
+
+    ## Below we restore the original 'key'
+    spe$key <- spe$key_original
+    spe$key_original <- NULL
+    head(spe$key)
 }
 }
diff --git a/man/add_qc_metrics.Rd b/man/add_qc_metrics.Rd
index 22e91df7..7623b2c2 100644
--- a/man/add_qc_metrics.Rd
+++ b/man/add_qc_metrics.Rd
@@ -95,7 +95,7 @@ spe_qc$our_low_lib_edge <- spe_qc$scran_low_lib_size & spe_qc$edge_distance < 5
 vis_clus(spe_qc, sample_id = "Br6432_ant", clustervar = "our_low_lib_edge")
 
 ## Clean up
-rm(spe_qc, spec_pre_qc)
+rm(spe_qc, spe_pre_qc, vars)
 
 }
 \author{
diff --git a/man/check_sce_layer.Rd b/man/check_sce_layer.Rd
index cac2d6c7..d2c9bf32 100644
--- a/man/check_sce_layer.Rd
+++ b/man/check_sce_layer.Rd
@@ -25,10 +25,11 @@ For more details please check the vignette documentation.
 }
 \examples{
 
-## Obtain the necessary data
+## Obtain example data from the HumanPilot project
+## (Maynard, Collado-Torres, et al, 2021)
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
 
-## Check the object
+## Check the pseudo-bulked data
 check_sce_layer(sce_layer)
 }
 \seealso{
diff --git a/man/check_spe.Rd b/man/check_spe.Rd
index ecaa9867..577afeec 100644
--- a/man/check_spe.Rd
+++ b/man/check_spe.Rd
@@ -10,11 +10,11 @@ check_spe(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{variables}{A \code{character()} vector of variable names expected to
 be present in \code{colData(spe)}.}
diff --git a/man/cluster_export.Rd b/man/cluster_export.Rd
index 613e5cdf..238cb5aa 100644
--- a/man/cluster_export.Rd
+++ b/man/cluster_export.Rd
@@ -12,11 +12,11 @@ cluster_export(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{cluster_var}{A \code{character(1)} with the name of the variable you wish to
 export.}
diff --git a/man/cluster_import.Rd b/man/cluster_import.Rd
index 778a73d8..2c7288fa 100644
--- a/man/cluster_import.Rd
+++ b/man/cluster_import.Rd
@@ -12,11 +12,11 @@ cluster_import(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{cluster_dir}{A \code{character(1)} specifying the output directory, similar
 to the \code{outs/analysis/clustering} produced by SpaceRanger.}
diff --git a/man/frame_limits.Rd b/man/frame_limits.Rd
index 8b5cbe77..9274af88 100644
--- a/man/frame_limits.Rd
+++ b/man/frame_limits.Rd
@@ -13,11 +13,11 @@ frame_limits(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{sampleid}{A \code{character(1)} specifying which sample to plot from
 \code{colData(spe)$sample_id} (formerly \code{colData(spe)$sample_name}).}
diff --git a/man/img_edit.Rd b/man/img_edit.Rd
index 699bea07..a2392bce 100644
--- a/man/img_edit.Rd
+++ b/man/img_edit.Rd
@@ -26,11 +26,11 @@ img_edit(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{sampleid}{A \code{character(1)} specifying which sample to plot from
 \code{colData(spe)$sample_id} (formerly \code{colData(spe)$sample_name}).}
diff --git a/man/img_update.Rd b/man/img_update.Rd
index 3d0c1315..b3b1ecdb 100644
--- a/man/img_update.Rd
+++ b/man/img_update.Rd
@@ -14,11 +14,11 @@ img_update(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{sampleid}{A \code{character(1)} specifying which sample to plot from
 \code{colData(spe)$sample_id} (formerly \code{colData(spe)$sample_name}).}
diff --git a/man/img_update_all.Rd b/man/img_update_all.Rd
index 2040e55b..a4d4f36c 100644
--- a/man/img_update_all.Rd
+++ b/man/img_update_all.Rd
@@ -13,11 +13,11 @@ img_update_all(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{image_id}{A \code{character(1)} with the name of the image ID you want to
 use in the background.}
diff --git a/man/locate_images.Rd b/man/locate_images.Rd
index 6041b6c8..58448fb8 100644
--- a/man/locate_images.Rd
+++ b/man/locate_images.Rd
@@ -7,11 +7,11 @@
 locate_images(spe, image_dir, image_pattern)
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{image_dir}{A \code{character(1)} specifying a path to a directory containing
 image files with the pattern \code{sampleID_pattern.png}.}
diff --git a/man/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.Rd b/man/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.Rd
index 11d2c849..2996d31a 100644
--- a/man/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.Rd
+++ b/man/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.Rd
@@ -19,8 +19,12 @@ and
 tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer
 }
 \description{
-Using the DLPFC snRNA-seq data from Matthew N Tran et al we computed
-enrichment t-statistics for the cell clusters. This is a subset of them
-used in examples such as in \code{\link[=layer_stat_cor_plot]{layer_stat_cor_plot()}}.
+Using the DLPFC snRNA-seq data from Matthew N Tran et al
+\url{https://doi.org/10.1016/j.neuron.2021.09.001} we computed
+enrichment t-statistics for the cell clusters. The Tran et al data has been
+subset to the top 100 DLPFC layer markers found in Maynard, Collado-Torres,
+et al 2021. This data is used in examples such as in
+\code{\link[=layer_stat_cor_plot]{layer_stat_cor_plot()}}. The Tran et al data is from the pre-print version
+of that project.
 }
 \keyword{datasets}
diff --git a/man/vis_clus.Rd b/man/vis_clus.Rd
index 10729e46..34513c66 100644
--- a/man/vis_clus.Rd
+++ b/man/vis_clus.Rd
@@ -21,11 +21,11 @@ vis_clus(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{sampleid}{A \code{character(1)} specifying which sample to plot from
 \code{colData(spe)$sample_id} (formerly \code{colData(spe)$sample_name}).}
diff --git a/man/vis_clus_p.Rd b/man/vis_clus_p.Rd
index 3706e6a2..b8202f1f 100644
--- a/man/vis_clus_p.Rd
+++ b/man/vis_clus_p.Rd
@@ -20,14 +20,14 @@ vis_clus_p(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
-\item{d}{A data.frame with the sample-level information. This is typically
-obtained using \code{cbind(colData(spe), spatialCoords(spe))}.}
+\item{d}{A \code{data.frame()} with the sample-level information. This is
+typically obtained using \code{cbind(colData(spe), spatialCoords(spe))}.}
 
 \item{clustervar}{A \code{character(1)} with the name of the \code{colData(spe)}
 column that has the cluster values.}
diff --git a/man/vis_gene.Rd b/man/vis_gene.Rd
index 2a6f94e6..bba4dc60 100644
--- a/man/vis_gene.Rd
+++ b/man/vis_gene.Rd
@@ -25,21 +25,21 @@ vis_gene(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{sampleid}{A \code{character(1)} specifying which sample to plot from
 \code{colData(spe)$sample_id} (formerly \code{colData(spe)$sample_name}).}
 
 \item{geneid}{A \code{character()} specifying the gene ID(s) stored in
-\code{rowData(spe)$gene_search} or a continuous variable(s) stored in \code{colData(spe)}
-to visualize. For each ID, if \code{rowData(spe)$gene_search} is missing, then
-\code{rownames(spe)} is used to search for the gene ID. When a vector of length > 1
-is supplied, the continuous variables are combined according to \code{multi_gene_method},
-producing a single value for each spot.}
+\code{rowData(spe)$gene_search} or a continuous variable(s) stored in
+\code{colData(spe)} to visualize. For each ID, if \code{rowData(spe)$gene_search} is
+missing, then \code{rownames(spe)} is used to search for the gene ID. When a
+vector of length > 1 is supplied, the continuous variables are combined
+according to \code{multi_gene_method}, producing a single value for each spot.}
 
 \item{spatial}{A \code{logical(1)} indicating whether to include the histology
 layer from \code{\link[=geom_spatial]{geom_spatial()}}. If you plan to use
@@ -81,8 +81,8 @@ alpha blending already, which will make non-NA values pop up more and the NA
 values will show with a lighter color. This behavior is lost when \code{alpha} is
 set to a non-\code{NA} value.}
 
-\item{multi_gene_method}{A \code{character(1)}: either "pca", "sparsity", or
-"z_score". This parameter controls how multiple continuous variables are
+\item{multi_gene_method}{A \code{character(1)}: either \code{"pca"}, \code{"sparsity"}, or
+\code{"z_score"}. This parameter controls how multiple continuous variables are
 combined for visualization, and only applies when \code{geneid} has length
 great than 1. \code{z_score}: to summarize multiple continuous variables, each is
 normalized to represent a Z-score. The multiple scores are then averaged.
diff --git a/man/vis_gene_p.Rd b/man/vis_gene_p.Rd
index c1115f71..d8fb4ea0 100644
--- a/man/vis_gene_p.Rd
+++ b/man/vis_gene_p.Rd
@@ -26,15 +26,15 @@ vis_gene_p(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
-\item{d}{A data.frame with the sample-level information. This is typically
-obtained using \code{cbind(colData(spe), spatialCoords(spe))}.
-The data.frame has to contain
+\item{d}{A \code{data.frame()} with the sample-level information. This is
+typically obtained using \code{cbind(colData(spe), spatialCoords(spe))}.
+The \code{data.frame} has to contain
 a column with the continuous variable data to plot stored under \code{d$COUNT}.}
 
 \item{sampleid}{A \code{character(1)} specifying which sample to plot from
@@ -84,7 +84,7 @@ A \link[ggplot2:ggplot]{ggplot2} object.
 This function visualizes the gene expression stored in \code{assays(spe)} or any
 continuous variable stored in \code{colData(spe)} for one given sample at the
 spot-level using (by default) the histology information on the background.
-This is the function that does all the plotting behind \code{\link[=vis_gene]{vis_gene()}}.
+This is the function that does all the plotting behind \code{\link[=vis_gene]{vis_gene()}}
 To visualize clusters (or any discrete variable) use \code{\link[=vis_clus_p]{vis_clus_p()}}.
 }
 \examples{
diff --git a/man/vis_grid_clus.Rd b/man/vis_grid_clus.Rd
index 19dd2c3a..af943564 100644
--- a/man/vis_grid_clus.Rd
+++ b/man/vis_grid_clus.Rd
@@ -25,11 +25,11 @@ vis_grid_clus(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{clustervar}{A \code{character(1)} with the name of the \code{colData(spe)}
 column that has the cluster values.}
diff --git a/man/vis_grid_gene.Rd b/man/vis_grid_gene.Rd
index a102cbbe..40b7461c 100644
--- a/man/vis_grid_gene.Rd
+++ b/man/vis_grid_gene.Rd
@@ -28,18 +28,18 @@ vis_grid_gene(
 )
 }
 \arguments{
-\item{spe}{Defaults to the output of
-\code{fetch_data(type = 'spe')}. This is a
+\item{spe}{A
 \link[SpatialExperiment:SpatialExperiment]{SpatialExperiment-class}
-object with the spot-level Visium data and information required for
-visualizing the histology. See \code{\link[=fetch_data]{fetch_data()}} for more details.}
+object. See \code{\link[=fetch_data]{fetch_data()}} for how to download some example objects or
+\code{\link[=read10xVisiumWrapper]{read10xVisiumWrapper()}} to read in \code{spaceranger --count} output files and
+build your own \code{spe} object.}
 
 \item{geneid}{A \code{character()} specifying the gene ID(s) stored in
-\code{rowData(spe)$gene_search} or a continuous variable(s) stored in \code{colData(spe)}
-to visualize. For each ID, if \code{rowData(spe)$gene_search} is missing, then
-\code{rownames(spe)} is used to search for the gene ID. When a vector of length > 1
-is supplied, the continuous variables are combined according to \code{multi_gene_method},
-producing a single value for each spot.}
+\code{rowData(spe)$gene_search} or a continuous variable(s) stored in
+\code{colData(spe)} to visualize. For each ID, if \code{rowData(spe)$gene_search} is
+missing, then \code{rownames(spe)} is used to search for the gene ID. When a
+vector of length > 1 is supplied, the continuous variables are combined
+according to \code{multi_gene_method}, producing a single value for each spot.}
 
 \item{pdf_file}{A \code{character(1)} specifying the path for the resulting PDF.}