diff --git a/articles/CellMembrane-Tutorial.html b/articles/CellMembrane-Tutorial.html index 75507d6a..1cad3064 100644 --- a/articles/CellMembrane-Tutorial.html +++ b/articles/CellMembrane-Tutorial.html @@ -81,7 +81,7 @@

CellMembrane Tutorial

GW McElfresh

-

2024-12-22

+

2024-12-23

Source: vignettes/CellMembrane-Tutorial.Rmd diff --git a/articles/Pseudobulking-and-Filtered-Contrasts.html b/articles/Pseudobulking-and-Filtered-Contrasts.html index f94a055e..342c41f8 100644 --- a/articles/Pseudobulking-and-Filtered-Contrasts.html +++ b/articles/Pseudobulking-and-Filtered-Contrasts.html @@ -81,7 +81,7 @@

Pseudobulking-and-Filtered-Contrasts

GW McElfresh

-

2024-12-22

+

2024-12-23

Source: vignettes/Pseudobulking-and-Filtered-Contrasts.Rmd diff --git a/pkgdown.yml b/pkgdown.yml index 795fd91f..a5d001fd 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,4 +4,4 @@ pkgdown_sha: ~ articles: CellMembrane-Tutorial: CellMembrane-Tutorial.html Pseudobulking-and-Filtered-Contrasts: Pseudobulking-and-Filtered-Contrasts.html -last_built: 2024-12-22T17:23Z +last_built: 2024-12-23T16:59Z diff --git a/reference/PlotTfData.html b/reference/PlotTfData.html new file mode 100644 index 00000000..1bfbf7ce --- /dev/null +++ b/reference/PlotTfData.html @@ -0,0 +1,117 @@ + +Plot TF Data — PlotTfData • CellMembrane + + +
+
+ + + +
+
+
+

Plot TF Data

+ Source: R/decoupleR.R + +
+ +
+

This will plot the results of decoupleR as a heatmap

+
+ +
+ 
PlotTfData(
+  seuratObj,
+  assayName = "tfsulm",
+  groupField = Seurat::Idents(seuratObj)
+)
+
+ +
+

Arguments

+ + +
seuratObj
+

A Seurat object.

+ + +
assayName
+

The source assay

+ + +
groupField
+

The field on which to group the results

+ +
+
+

Value

+

The pheatmap plot object

+
+ +
+ +
+ + +
+ + + + + + + + diff --git a/reference/RunDecoupleR.html b/reference/RunDecoupleR.html new file mode 100644 index 00000000..401fd81b --- /dev/null +++ b/reference/RunDecoupleR.html @@ -0,0 +1,122 @@ + +Run decoupleR — RunDecoupleR • CellMembrane + + +
+
+ + + +
+
+
+

Run decoupleR

+ Source: R/decoupleR.R + +
+ +
+

This will run decoupleR to infer TF

+
+ +
+ 
RunDecoupleR(
+  seuratObj,
+  sourceAssay = "RNA",
+  targetAssay = "tfsulm",
+  organism = "human"
+)
+
+ +
+

Arguments

+ + +
seuratObj
+

A Seurat object.

+ + +
sourceAssay
+

The source assay

+ + +
targetAssay
+

The target assay to store results

+ + +
organism
+

Passed directly to decoupleR::get_collectri()

+ +
+
+

Value

+

The seurat object

+
+ +
+ +
+ + +
+ + + + + + + + diff --git a/reference/index.html b/reference/index.html index f9659bbb..0ff7e571 100644 --- a/reference/index.html +++ b/reference/index.html @@ -272,6 +272,10 @@

All functions PlotSeuratVariables()

Plot Seurat Variables

+ +

PlotTfData()

+ +

Plot TF Data

Plot_SDAScoresPerFeature()

@@ -332,6 +336,10 @@

All functions RunCsCore()

Run CS-CORE

+ +

RunDecoupleR()

+ +

Run decoupleR

RunEscape()

diff --git a/sitemap.xml b/sitemap.xml index 653e4803..bd70f462 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -58,6 +58,7 @@ /reference/PlotAverageAdtCounts.html /reference/PlotSdaCellScores.html /reference/PlotSeuratVariables.html +/reference/PlotTfData.html /reference/Plot_SDAScoresPerFeature.html /reference/PredictScTourPseudotime.html /reference/PseudobulkSeurat.html @@ -73,6 +74,7 @@ /reference/ResolveLocGenes.html /reference/RunCoNGA.html /reference/RunCsCore.html +/reference/RunDecoupleR.html /reference/RunEscape.html /reference/RunFilteredContrasts.html /reference/RunPHATE.html