From ad7b0e6dee1ebc473622592fc25b9db847e35905 Mon Sep 17 00:00:00 2001 From: lahuuki <36641297+lahuuki@users.noreply.github.com> Date: Wed, 7 Aug 2024 17:35:51 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/DeconvoBuddies@4192530e91e294ddfd25e1e6b09e1c2a890dd574?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/DeconvoBuddies.html | 14 +++++++------- articles/Deconvolution_Benchmark_DLPFC.html | 14 +++++++------- articles/Marker_Finding.html | 12 ++++++------ pkgdown.yml | 2 +- reference/dot-get_mean_ratio2.html | 2 +- reference/fetch_deconvo_data.html | 4 ++-- reference/findMarkers_1vAll.html | 6 +++--- reference/get_mean_ratio.html | 7 ++++--- reference/plot_gene_express.html | 2 +- reference/plot_marker_express.html | 2 +- reference/plot_marker_express_ALL.html | 2 +- reference/plot_marker_express_List.html | 2 +- 12 files changed, 35 insertions(+), 34 deletions(-) diff --git a/articles/DeconvoBuddies.html b/articles/DeconvoBuddies.html index 1f752b7..4a02825 100644 --- a/articles/DeconvoBuddies.html +++ b/articles/DeconvoBuddies.html @@ -220,7 +220,7 @@

Access Data
 ## Access and snRNA-seq example data
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-08-07 17:19:42.389455 loading file /github/home/.cache/R/BiocFileCache/3fa46dab753_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-08-07 17:33:45.703235 loading file /github/home/.cache/R/BiocFileCache/4a1ec11882_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 
 ## Explore snRNA-seq data in sce_DLPFC_example
 sce_DLPFC_example
@@ -239,7 +239,7 @@ 
Access Data## Access Bulk RNA-seq data
 if (!exists("rse_gene")) rse_gene <- fetch_deconvo_data("rse_gene")
-#> 2024-08-07 17:19:44.000028 loading file /github/home/.cache/R/BiocFileCache/3fa7e764288_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
+#> 2024-08-07 17:33:47.478342 loading file /github/home/.cache/R/BiocFileCache/4a1de5efa9_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
 
 ## Explore bulk data in rse_gene
 rse_gene
@@ -470,9 +470,9 @@ 
Reproducibilitylibrary("knitr")
 knit("DeconvoBuddies.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-08-07 17:19:48 UTC"
+
#> [1] "2024-08-07 17:33:51 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 18.249 secs
+
#> Time difference of 18.582 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -538,7 +538,7 @@ 
Reproducibility#>  dplyr                * 1.1.4      2023-11-17 [1] RSPM (R 4.4.0)
 #>  dqrng                  0.4.1      2024-05-28 [1] RSPM (R 4.4.0)
 #>  DT                     0.33       2024-04-04 [1] RSPM (R 4.4.0)
-#>  edgeR                  4.3.7      2024-07-31 [1] Bioconductor 3.20 (R 4.4.1)
+#>  edgeR                  4.3.8      2024-08-06 [1] Bioconductor 3.20 (R 4.4.1)
 #>  evaluate               0.24.0     2024-06-10 [2] RSPM (R 4.4.0)
 #>  ExperimentHub          2.13.1     2024-07-31 [1] Bioconductor 3.20 (R 4.4.1)
 #>  fansi                  1.0.6      2023-12-08 [2] RSPM (R 4.4.0)
@@ -618,7 +618,7 @@ 
Reproducibility#>  RSQLite                2.3.7      2024-05-27 [1] RSPM (R 4.4.0)
 #>  rsvd                   1.0.5      2021-04-16 [1] RSPM (R 4.4.0)
 #>  rtracklayer            1.65.0     2024-05-01 [1] Bioconductor 3.20 (R 4.4.0)
-#>  S4Arrays               1.5.5      2024-07-21 [1] Bioconductor 3.20 (R 4.4.1)
+#>  S4Arrays               1.5.7      2024-08-06 [1] Bioconductor 3.20 (R 4.4.1)
 #>  S4Vectors            * 0.43.2     2024-07-17 [1] Bioconductor 3.20 (R 4.4.1)
 #>  sass                   0.4.9      2024-03-15 [2] RSPM (R 4.4.0)
 #>  ScaledMatrix           1.13.0     2024-05-01 [1] Bioconductor 3.20 (R 4.4.0)
@@ -631,7 +631,7 @@ 
Reproducibility#>  shinyWidgets           0.8.6      2024-04-24 [1] RSPM (R 4.4.0)
 #>  SingleCellExperiment   1.27.2     2024-05-24 [1] Bioconductor 3.20 (R 4.4.0)
 #>  spam                   2.10-0     2023-10-23 [1] RSPM (R 4.4.0)
-#>  SparseArray            1.5.30     2024-08-02 [1] Bioconductor 3.20 (R 4.4.1)
+#>  SparseArray            1.5.31     2024-08-04 [1] Bioconductor 3.20 (R 4.4.1)
 #>  SpatialExperiment      1.15.1     2024-06-20 [1] Bioconductor 3.20 (R 4.4.0)
 #>  spatialLIBD            1.17.8     2024-07-25 [1] Bioconductor 3.20 (R 4.4.1)
 #>  statmod                1.5.0      2023-01-06 [1] RSPM (R 4.4.0)
diff --git a/articles/Deconvolution_Benchmark_DLPFC.html b/articles/Deconvolution_Benchmark_DLPFC.html
index 2fefbc9..b842b41 100644
--- a/articles/Deconvolution_Benchmark_DLPFC.html
+++ b/articles/Deconvolution_Benchmark_DLPFC.html
@@ -261,7 +261,7 @@ 
Bulk RNA-seq data
 ## use fetch deconvon data to load rse_gene
 rse_gene <- fetch_deconvo_data("rse_gene")
-#> 2024-08-07 17:20:04.139751 loading file /github/home/.cache/R/BiocFileCache/3fa7e764288_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
+#> 2024-08-07 17:34:07.847847 loading file /github/home/.cache/R/BiocFileCache/4a1de5efa9_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
 rse_gene
 #> class: RangedSummarizedExperiment 
 #> dim: 21745 110 
@@ -297,7 +297,7 @@ 
Reference snRNA-seq data
 ## Use spatialLIBD to fetch the snRNA-seq dataset
 sce_path_zip <- fetch_deconvo_data("sce")
-#> 2024-08-07 17:20:05.652079 loading file /github/home/.cache/R/BiocFileCache/3fa309b34dd_sce_DLPFC_annotated.zip%3Fdl%3D1
+#> 2024-08-07 17:34:09.528637 loading file /github/home/.cache/R/BiocFileCache/4a1415db437_sce_DLPFC_annotated.zip%3Fdl%3D1
 
 ## unzip and load the data
 sce_path <- unzip(sce_path_zip, exdir = tempdir())
@@ -762,9 +762,9 @@ 
Reproducibilitylibrary("knitr")
 knit("Deconvolution_Benchmark_DLPFC.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-08-07 17:21:03 UTC"

+
#> [1] "2024-08-07 17:35:08 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 1.182 mins

+
#> Time difference of 1.214 mins

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -831,7 +831,7 @@ 
Reproducibility#>  dplyr                * 1.1.4      2023-11-17 [1] RSPM (R 4.4.0)
 #>  dqrng                  0.4.1      2024-05-28 [1] RSPM (R 4.4.0)
 #>  DT                     0.33       2024-04-04 [1] RSPM (R 4.4.0)
-#>  edgeR                  4.3.7      2024-07-31 [1] Bioconductor 3.20 (R 4.4.1)
+#>  edgeR                  4.3.8      2024-08-06 [1] Bioconductor 3.20 (R 4.4.1)
 #>  evaluate               0.24.0     2024-06-10 [2] RSPM (R 4.4.0)
 #>  ExperimentHub          2.13.1     2024-07-31 [1] Bioconductor 3.20 (R 4.4.1)
 #>  fansi                  1.0.6      2023-12-08 [2] RSPM (R 4.4.0)
@@ -919,7 +919,7 @@ 
Reproducibility#>  RSQLite                2.3.7      2024-05-27 [1] RSPM (R 4.4.0)
 #>  rsvd                   1.0.5      2021-04-16 [1] RSPM (R 4.4.0)
 #>  rtracklayer            1.65.0     2024-05-01 [1] Bioconductor 3.20 (R 4.4.0)
-#>  S4Arrays               1.5.5      2024-07-21 [1] Bioconductor 3.20 (R 4.4.1)
+#>  S4Arrays               1.5.7      2024-08-06 [1] Bioconductor 3.20 (R 4.4.1)
 #>  S4Vectors            * 0.43.2     2024-07-17 [1] Bioconductor 3.20 (R 4.4.1)
 #>  sass                   0.4.9      2024-03-15 [2] RSPM (R 4.4.0)
 #>  ScaledMatrix           1.13.0     2024-05-01 [1] Bioconductor 3.20 (R 4.4.0)
@@ -932,7 +932,7 @@ 
Reproducibility#>  shinyWidgets           0.8.6      2024-04-24 [1] RSPM (R 4.4.0)
 #>  SingleCellExperiment * 1.27.2     2024-05-24 [1] Bioconductor 3.20 (R 4.4.0)
 #>  spam                   2.10-0     2023-10-23 [1] RSPM (R 4.4.0)
-#>  SparseArray            1.5.30     2024-08-02 [1] Bioconductor 3.20 (R 4.4.1)
+#>  SparseArray            1.5.31     2024-08-04 [1] Bioconductor 3.20 (R 4.4.1)
 #>  SpatialExperiment    * 1.15.1     2024-06-20 [1] Bioconductor 3.20 (R 4.4.0)
 #>  spatialLIBD          * 1.17.8     2024-07-25 [1] Bioconductor 3.20 (R 4.4.1)
 #>  statmod                1.5.0      2023-01-06 [1] RSPM (R 4.4.0)
diff --git a/articles/Marker_Finding.html b/articles/Marker_Finding.html
index 05443b4..54c0154 100644
--- a/articles/Marker_Finding.html
+++ b/articles/Marker_Finding.html
@@ -186,7 +186,7 @@ 
2. Download DLPFC snRNA-seq data.
 ## Use spatialLIBD to fetch the snRNA-seq dataset
 sce_path_zip <- fetch_deconvo_data("sce")
-#> 2024-08-07 17:21:25.344741 loading file /github/home/.cache/R/BiocFileCache/3fa309b34dd_sce_DLPFC_annotated.zip%3Fdl%3D1
+#> 2024-08-07 17:35:26.553214 loading file /github/home/.cache/R/BiocFileCache/4a1415db437_sce_DLPFC_annotated.zip%3Fdl%3D1
 
 ## unzip and load the data
 sce_path <- unzip(sce_path_zip, exdir = tempdir())
@@ -251,9 +251,9 @@ 
Reproducibilitylibrary("knitr")
 knit("Marker_Finding.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-08-07 17:21:46 UTC"

+
#> [1] "2024-08-07 17:35:41 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 34.578 secs

+
#> Time difference of 27.362 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -319,7 +319,7 @@ 
Reproducibility#>  dplyr                * 1.1.4      2023-11-17 [1] RSPM (R 4.4.0)
 #>  dqrng                  0.4.1      2024-05-28 [1] RSPM (R 4.4.0)
 #>  DT                     0.33       2024-04-04 [1] RSPM (R 4.4.0)
-#>  edgeR                  4.3.7      2024-07-31 [1] Bioconductor 3.20 (R 4.4.1)
+#>  edgeR                  4.3.8      2024-08-06 [1] Bioconductor 3.20 (R 4.4.1)
 #>  evaluate               0.24.0     2024-06-10 [2] RSPM (R 4.4.0)
 #>  ExperimentHub          2.13.1     2024-07-31 [1] Bioconductor 3.20 (R 4.4.1)
 #>  fansi                  1.0.6      2023-12-08 [2] RSPM (R 4.4.0)
@@ -399,7 +399,7 @@ 
Reproducibility#>  RSQLite                2.3.7      2024-05-27 [1] RSPM (R 4.4.0)
 #>  rsvd                   1.0.5      2021-04-16 [1] RSPM (R 4.4.0)
 #>  rtracklayer            1.65.0     2024-05-01 [1] Bioconductor 3.20 (R 4.4.0)
-#>  S4Arrays               1.5.5      2024-07-21 [1] Bioconductor 3.20 (R 4.4.1)
+#>  S4Arrays               1.5.7      2024-08-06 [1] Bioconductor 3.20 (R 4.4.1)
 #>  S4Vectors            * 0.43.2     2024-07-17 [1] Bioconductor 3.20 (R 4.4.1)
 #>  sass                   0.4.9      2024-03-15 [2] RSPM (R 4.4.0)
 #>  ScaledMatrix           1.13.0     2024-05-01 [1] Bioconductor 3.20 (R 4.4.0)
@@ -412,7 +412,7 @@ 
Reproducibility#>  shinyWidgets           0.8.6      2024-04-24 [1] RSPM (R 4.4.0)
 #>  SingleCellExperiment * 1.27.2     2024-05-24 [1] Bioconductor 3.20 (R 4.4.0)
 #>  spam                   2.10-0     2023-10-23 [1] RSPM (R 4.4.0)
-#>  SparseArray            1.5.30     2024-08-02 [1] Bioconductor 3.20 (R 4.4.1)
+#>  SparseArray            1.5.31     2024-08-04 [1] Bioconductor 3.20 (R 4.4.1)
 #>  SpatialExperiment    * 1.15.1     2024-06-20 [1] Bioconductor 3.20 (R 4.4.0)
 #>  spatialLIBD          * 1.17.8     2024-07-25 [1] Bioconductor 3.20 (R 4.4.1)
 #>  statmod                1.5.0      2023-01-06 [1] RSPM (R 4.4.0)
diff --git a/pkgdown.yml b/pkgdown.yml
index 969f743..69bd4aa 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,4 +5,4 @@ articles:
   DeconvoBuddies: DeconvoBuddies.html
   Deconvolution_Benchmark_DLPFC: Deconvolution_Benchmark_DLPFC.html
   Marker_Finding: Marker_Finding.html
-last_built: 2024-08-07T17:18Z
+last_built: 2024-08-07T17:32Z
diff --git a/reference/dot-get_mean_ratio2.html b/reference/dot-get_mean_ratio2.html
index f3db3a7..a2ba3ce 100644
--- a/reference/dot-get_mean_ratio2.html
+++ b/reference/dot-get_mean_ratio2.html
@@ -117,7 +117,7 @@ 
Details

     
Examples

     
#' ## load example SingleCellExperiment
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-08-07 17:18:52.414898 loading file /github/home/.cache/R/BiocFileCache/3fa46dab753_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-08-07 17:32:53.195728 loading file /github/home/.cache/R/BiocFileCache/4a1ec11882_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 
 ## Get the mean ratio for each gene for each cell type defined in `cellType_broad_hc`
 .get_mean_ratio2(sce_DLPFC_example, cellType_col = "cellType_broad_hc")
diff --git a/reference/fetch_deconvo_data.html b/reference/fetch_deconvo_data.html
index f6ecf40..9eb8fbc 100644
--- a/reference/fetch_deconvo_data.html
+++ b/reference/fetch_deconvo_data.html
@@ -132,7 +132,7 @@ 
Examples

 ## A RangedSummarizedExperiment (41.16 MB)
 
 if (!exists("rse-gene")) rse_gene <- fetch_deconvo_data("rse_gene")
-#> 2024-08-07 17:18:54.753519 loading file /github/home/.cache/R/BiocFileCache/3fa7e764288_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
+#> 2024-08-07 17:32:55.846502 loading file /github/home/.cache/R/BiocFileCache/4a1de5efa9_rse_gene.Rdata%3Frlkey%3Dsw2djr71y954yw4o3xrmjv59b%26dl%3D1
 
 ## explore data
 rse_gene
@@ -160,7 +160,7 @@ 
Examples

 ## load example snRNA-seq data
 ## A SingleCellExperiment (4.79 MB)
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-08-07 17:18:56.423686 loading file /github/home/.cache/R/BiocFileCache/3fa46dab753_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-08-07 17:32:57.693436 loading file /github/home/.cache/R/BiocFileCache/4a1ec11882_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 
 
 sce_DLPFC_example
diff --git a/reference/findMarkers_1vAll.html b/reference/findMarkers_1vAll.html
index 62fbfab..cb26561 100644
--- a/reference/findMarkers_1vAll.html
+++ b/reference/findMarkers_1vAll.html
@@ -117,9 +117,9 @@ 
Value

     

     
Examples

     
markers_1vAll <- findMarkers_1vAll(sce_ab)
-#> A - '2024-08-07 17:18:57.247372
-#> B - '2024-08-07 17:18:57.558917
-#> Building Table - 2024-08-07 17:18:57.712286
+#> A - '2024-08-07 17:32:58.690142
+#> B - '2024-08-07 17:32:59.008849
+#> Building Table - 2024-08-07 17:32:59.164719
 #> ** Done! **
 head(markers_1vAll)
 #> # A tibble: 6 × 8
diff --git a/reference/get_mean_ratio.html b/reference/get_mean_ratio.html
index 37cf39c..e96dc51 100644
--- a/reference/get_mean_ratio.html
+++ b/reference/get_mean_ratio.html
@@ -92,7 +92,7 @@ 
Arguments

 
cellType_col

 
A character(1) name of the column in the
 colData() of sce that
-denotes the cell type or group of interest

+denotes the cell type or group of interest.

 
 
 
assay_name

@@ -126,14 +126,15 @@ 
Value

 

     

     
Details

-    
Improved argument names and documentaion, but same functionalty from get_mean_ratio2().

+    
Note if a cell type has < 10 cells the MeanRatio results may be unstable.
+See rational in OSCA: https://bioconductor.org/books/3.19/OSCA.multisample/multi-sample-comparisons.html#performing-the-de-analysis

     

 
     

     
Examples

     
## load example SingleCellExperiment
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-08-07 17:18:58.840072 loading file /github/home/.cache/R/BiocFileCache/3fa46dab753_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-08-07 17:33:00.419412 loading file /github/home/.cache/R/BiocFileCache/4a1ec11882_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 ## Explore properties of the sce object
 sce_DLPFC_example
 #> class: SingleCellExperiment 
diff --git a/reference/plot_gene_express.html b/reference/plot_gene_express.html
index f7bec87..413056c 100644
--- a/reference/plot_gene_express.html
+++ b/reference/plot_gene_express.html
@@ -144,7 +144,7 @@ 
Examples

 
 
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-08-07 17:19:04.577604 loading file /github/home/.cache/R/BiocFileCache/3fa46dab753_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-08-07 17:33:06.529501 loading file /github/home/.cache/R/BiocFileCache/4a1ec11882_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 ## plot expression of two genes
 plot_gene_express(sce = sce_DLPFC_example, category = "cellType_broad_hc", genes = c("GAD2", "CD22"))
 #> No summary function supplied, defaulting to `mean_se()`
diff --git a/reference/plot_marker_express.html b/reference/plot_marker_express.html
index cdfda87..9dc7169 100644
--- a/reference/plot_marker_express.html
+++ b/reference/plot_marker_express.html
@@ -155,7 +155,7 @@ 
See also

     

     
Examples

     
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-08-07 17:19:07.831478 loading file /github/home/.cache/R/BiocFileCache/3fa46dab753_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-08-07 17:33:09.904147 loading file /github/home/.cache/R/BiocFileCache/4a1ec11882_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 ## plot the top markers for Astrocytes in
 plot_marker_express(
     sce = sce_DLPFC_example,
diff --git a/reference/plot_marker_express_ALL.html b/reference/plot_marker_express_ALL.html
index 5fb8855..6749dc8 100644
--- a/reference/plot_marker_express_ALL.html
+++ b/reference/plot_marker_express_ALL.html
@@ -153,7 +153,7 @@ 
See also

     
Examples

     
#' ## Fetch sce example data
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
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 # Plot marker gene expression to PDF, one page per cell type in stats
 pdf_file <- tempfile("test_marker_expression_ALL", fileext = ".pdf")
diff --git a/reference/plot_marker_express_List.html b/reference/plot_marker_express_List.html
index ef1ca54..afdac08 100644
--- a/reference/plot_marker_express_List.html
+++ b/reference/plot_marker_express_List.html
@@ -134,7 +134,7 @@ 
See also

     
Examples

     
## Fetch sce example data
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
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 ## Create list-of-lists of genes to plot, names of sub-list become title of page
 my_gene_list <- list(Inhib = c("GAD2", "SAMD5"), Astro = c("RGS20", "PRDM16"))