From 6adcbedb85ed35f66963d05c87eca541ecf32ada Mon Sep 17 00:00:00 2001 From: samuel-marsh Date: Fri, 6 Dec 2024 11:32:40 -0500 Subject: [PATCH] update site --- docs/articles/Gene_Expression_Plotting.html | 31 ++++++++++----------- docs/articles/Update_Gene_Symbols.html | 10 ++++--- docs/pkgdown.yml | 2 +- inst/pkgdown.yml | 2 +- 4 files changed, 22 insertions(+), 23 deletions(-) diff --git a/docs/articles/Gene_Expression_Plotting.html b/docs/articles/Gene_Expression_Plotting.html index 05195e170..3111a8ab3 100644 --- a/docs/articles/Gene_Expression_Plotting.html +++ b/docs/articles/Gene_Expression_Plotting.html @@ -1628,9 +1628,6 @@

Heatmaps# Or called within the `DoHeatmap` function. DoHeatmap(object = marsh_mouse_micro, features = micro_markers, cells = Random_Cells_Downsample(seurat_object = marsh_mouse_micro, num_cells = 150, allow_lower = T)) -
-DoHeatmap(object = marsh_mouse_micro, features = micro_markers, cells = Random_Cells_Downsample(seurat_object = marsh_mouse_micro,
-    num_cells = 150, allow_lower = T))
*Much easier now to see expression across all clusters.*

Much easier now to see expression across all clusters. @@ -1666,7 +1663,7 @@

New default color palettes

To best demonstrate rationale for this I’m going to use over-clustered version of the marsh_mouse_micro object.

-
+
 DimPlot(object = marsh_mouse_over)
 DimPlot_scCustom(seurat_object = marsh_mouse_over)

 

@@ -1686,7 +1683,7 @@ 
Shuffle Points
 
Here is example when plotting by donor in the human dataset to
 determine how well the dataset integration worked.

-
+
 DimPlot(object = marsh_human_pm, group.by = "sample_id")
 DimPlot_scCustom(seurat_object = marsh_human_pm, group.by = "sample_id")

 

@@ -1703,7 +1700,7 @@ 
Split DimPlotsWhen plotting a split plot Seurat::DimPlot() simplifies
 the axes by implementing shared axes depending on the number of columns
 specified.

-
+
 DimPlot(object = pbmc, split.by = "treatment")
 DimPlot(object = pbmc, split.by = "sample_id", ncol = 4)

 

@@ -1717,7 +1714,7 @@ 
Split DimPlotsBy default when using split.by with
 DimPlot_scCustom the layout is returned with an axes for
 each plot to make visualization of large numbers of splits easier.

-
+
 DimPlot_scCustom(seurat_object = pbmc, split.by = "treatment", num_columns = 4, repel = TRUE)

 

 *Simplified visualization without having to think about the number of variables that are being plotted.*

@@ -1729,7 +1726,7 @@ 
Split DimPlotsDimPlot_scCustom by supplying
 split_seurat = TRUE

-
+
 DimPlot_scCustom(seurat_object = pbmc, split.by = "treatment", num_columns = 4, repel = TRUE, split_seurat = TRUE)

 

 

@@ -1740,7 +1737,7 @@ 
Figure PlottingDimPlot_scCustom simply set
 figure_plot = TRUE.

-
+
 DimPlot_scCustom(seurat_object = pbmc, figure_plot = TRUE)

 

 

@@ -1759,7 +1756,7 @@ 
Highlight Cluster(s)
+
 Cluster_Highlight_Plot(seurat_object = marsh_mouse_over, cluster_name = "7", highlight_color = "navy",
     background_color = "lightgray")
 
@@ -1776,7 +1773,7 @@ 
Highlight 2+ clusters in the same
 

 
Cluster_Highlight_Plot() also supports the ability to
 plot multiple identities in the same plot.

-
+
 Cluster_Highlight_Plot(seurat_object = marsh_mouse_over, cluster_name = c("7", "8"), highlight_color = c("navy",
     "forestgreen"))

 

@@ -1794,7 +1791,7 @@ 
Highlight Meta Data
+
 Meta_Highlight_Plot(seurat_object = marsh_mouse_micro, meta_data_column = "Transcription_Method",
     meta_data_highlight = "ENZYMATIC_NONE", highlight_color = "firebrick", background_color = "lightgray")

 

@@ -1805,7 +1802,7 @@ 
Highlight 2+ factor levels i
 levels from the same meta data column in the same plot, similar to
 plotting multiple identities with
 Cluster_Highlight_Plot()

-
+
 Meta_Highlight_Plot(seurat_object = marsh_mouse_micro, meta_data_column = "Transcription_Method",
     meta_data_highlight = c("ENZYMATIC_NONE", "DOUNCE_NONE"), highlight_color = c("firebrick", "dodgerblue"),
     background_color = "lightgray")

@@ -1822,7 +1819,7 @@ 
Highlight Cellscells_highlight parameter must be a named list.

 
Let’s say we want to highlight cells with expression of
 MS4A1 above certain threshold.

-
+
 # Get cell names
 MS4A1 <- WhichCells(object = pbmc, expression = MS4A1 > 3)
 
@@ -1839,7 +1836,7 @@ 
Highlight 2+ sets of cells i
 sets of cells in the same plot, similar to plotting multiple identities
 with
 Cluster_Highlight_Plot()/Meta_Highlight_Plot().

-
+
 # Get cell names and make list
 MS4A1 <- WhichCells(object = pbmc, expression = MS4A1 > 3)
 GZMB <- WhichCells(object = pbmc, expression = GZMB > 3)
@@ -1856,7 +1853,7 @@ 
DimPlot Layout Plots
+
 DimPlot_All_Samples(seurat_object = pbmc, meta_data_column = "sample_id", num_col = 3, pt.size = 0.5)

 

 *Visualize all samples in simple plot layout.*

@@ -1865,7 +1862,7 @@ 
DimPlot Layout Plots
+
 DimPlot_All_Samples(seurat_object = marsh_mouse_micro, meta_data_column = "Transcription", num_col = 2,
     pt.size = 0.5, color = c("firebrick3", "dodgerblue3"))

 

diff --git a/docs/articles/Update_Gene_Symbols.html b/docs/articles/Update_Gene_Symbols.html
index abd1da447..8696ab993 100644
--- a/docs/articles/Update_Gene_Symbols.html
+++ b/docs/articles/Update_Gene_Symbols.html
@@ -258,7 +258,9 @@ 
Inappropriate renamingLet’s run our test symbol set:

 
 results <- Updated_HGNC_Symbols(input_data = test_symbols)

-
## Input features contained 3 gene symbols
+
## Downloading HGNC data from:
+## https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
+## Input features contained 3 gene symbols
 ## ✔ 3 were already approved symbols.
 ## → 0 were updated to approved symbol.
 ## ✖ 0 were not found in HGNC dataset and remain unchanged.

@@ -349,12 +351,12 @@ 
Inappropriate renamingtic()
 results <- Updated_HGNC_Symbols(input_data = features)

 
## Input features contained 36,601 gene symbols
-## ✔ 23,261 were already approved symbols.
-## → 749 were updated to approved symbol.
+## ✔ 23,260 were already approved symbols.
+## → 750 were updated to approved symbol.
 ## ✖ 12,591 were not found in HGNC dataset and remain unchanged.

 
 toc()

-
## 0.806 sec elapsed

+
## 0.891 sec elapsed

 

 

 
Examining the Results
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 0ffa5e706..b4e59bd6a 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -20,7 +20,7 @@ articles:
   Spatial_Plotting: Spatial_Plotting.html
   Statistics: Statistics.html
   Update_Gene_Symbols: Update_Gene_Symbols.html
-last_built: 2024-12-06T15:33Z
+last_built: 2024-12-06T16:13Z
 urls:
   reference: https://samuel-marsh.github.io/scCustomize/reference
   article: https://samuel-marsh.github.io/scCustomize/articles
diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml
index 0ffa5e706..b4e59bd6a 100644
--- a/inst/pkgdown.yml
+++ b/inst/pkgdown.yml
@@ -20,7 +20,7 @@ articles:
   Spatial_Plotting: Spatial_Plotting.html
   Statistics: Statistics.html
   Update_Gene_Symbols: Update_Gene_Symbols.html
-last_built: 2024-12-06T15:33Z
+last_built: 2024-12-06T16:13Z
 urls:
   reference: https://samuel-marsh.github.io/scCustomize/reference
   article: https://samuel-marsh.github.io/scCustomize/articles