scSidekick - Feature Expression: PlotFeaturePlots & PlotMultiFeature
04_feature_expression.RmdOverview
Two functions for visualizing gene expression on UMAP (or any reduction):
-
PlotFeaturePlots()- one panel per gene × split group. Saves to disk by convention; aliasGenerateFeatureMaps(). -
PlotMultiFeature()- co-expression of several genes on a single panel (gene mode, intersection mode, or continuous scale mode).
PlotFeaturePlots
3. Split by donor - one column per donor
split.by creates one column per level. Combined with
multiple features, this produces a gene × donor grid.
Pain point fixed. Seurat’s
FeaturePlot(..., split.by =)renders the panels with no color legend at all - you can’t tell what the colors mean, and the common& RestoreLegend()workaround attaches a guide that doesn’t match the data.PlotFeaturePlots()keeps one shared, accurate color scale across every panel, so expression is directly comparable across conditions.
PlotFeaturePlots(bmcite,
features = c("CD3E", "NKG7", "CD79A"),
split.by = "donor")4. Cluster labels overlay
label = TRUE prints cell-type labels at cluster
centroids, so you can immediately connect expression hotspots to their
identity.
PlotFeaturePlots(bmcite,
features = c("CD3E", "CD79A"),
label = TRUE,
label.by = "celltype.l1")
5. Multiple split.by - iterate automatically
Passing a vector to split.by generates one complete
figure per split variable.
PlotFeaturePlots(bmcite,
features = c("CD3E", "NKG7", "CD79A"),
split.by = c("lane"),row.by = "donor",layout_method = "metadata")
PlotMultiFeature
Mode 1 - Gene mode (default)
Each gene gets a distinct color. Cells expressing a gene above
threshold are colored accordingly; cells expressing more
than one gene get a blended color. A single UMAP panel shows all
lineages at once.
PlotMultiFeature(bmcite,
features = c("CD3E", "CD79A", "LYZ", "NKG7") )
Mode 2 - Intersection mode
Highlights only cells that co-express all listed genes above the cutoff. Useful for identifying rare dual-positive populations.
PlotMultiFeature(bmcite,
features = c("CD3E", "CD8A"),
plot_mode = "intersection",
pct_cutoff = 0.5,
intersection_label = "CD3+CD8+ T cells")
Mode 3 - Scale mode
Plots a single gene (or averaged signature) as a continuous gradient.
Equivalent to FeaturePlot() but integrated with the
scSidekick saving pipeline.
PlotMultiFeature(bmcite,
features = "CD3E",
plot_mode = "scale")
Parameter reference - PlotFeaturePlots
| Parameter | Type | Default | Description |
|---|---|---|---|
features |
character vector | required | Genes to plot |
split.by |
character (vector) | NULL |
Variable(s) for column splitting |
label |
logical | FALSE |
Add group labels at centroids |
label_by |
character | NULL |
Metadata column for centroid labels |
output_dir |
character | NULL |
Directory for saving |
object_name |
character | "" |
Label used in filenames |
subset_name |
character | "" |
Sub-label used in filenames |
file_name |
character | NULL |
Override the auto-built saved file name |
timestamp |
logical | FALSE |
Append a _YYYYMMDD-HHMMSS stamp to the saved file name
so repeated runs are versioned instead of overwritten |
Parameter reference - PlotMultiFeature
| Parameter | Type | Default | Description |
|---|---|---|---|
features |
character vector | required | Genes to co-visualize |
plot_mode |
character | "gene" |
"gene", "intersection", or
"scale"
|
colors |
character vector | NULL |
Colors per gene (gene mode) |
threshold |
numeric | 0.0125 |
Min expression to count a cell as “expressing” |
pct_cutoff |
numeric | 0.3 |
Co-expression cutoff (intersection mode) |
intersection_label |
character | NULL |
Label for co-expressing population |
output_dir |
character | NULL |
Directory for saving |
file_name |
character | NULL |
Override the auto-built saved file name |
timestamp |
logical | FALSE |
Append a _YYYYMMDD-HHMMSS stamp to the saved file name
so repeated runs are versioned instead of overwritten |
See also
- Vignette 03:
PlotDimPlots- cell-type UMAP without expression overlay - Vignette 05:
GroupHeatmap,FastDotPlot- expression across clusters - Vignette 07:
PlotSpatialFeaturePlots- same concept for spatial data
Session info
## R version 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS 15.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/Chicago
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] dplyr_1.1.4 stxBrain.SeuratData_0.1.2
## [3] pbmc3k.SeuratData_3.1.4 panc8.SeuratData_3.0.2
## [5] ifnb.SeuratData_3.1.0 bmcite.SeuratData_0.3.0
## [7] SeuratData_0.2.2 Seurat_5.2.1
## [9] SeuratObject_5.1.0 sp_2.1-3
## [11] scSidekick_1.2.0
##
## loaded via a namespace (and not attached):
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