Visualize factor expression and gene loading
Usage
plotGeneLoadings(
object,
markerTable,
useFactor,
useDimRed = NULL,
nLabel = 15,
nPlot = 30,
...
)
plotGeneLoadingRank(
object,
markerTable,
useFactor,
nLabel = 15,
nPlot = 30,
...
)
Arguments
- object
A liger object with valid factorization result.
- markerTable
Returned result of
getFactorMarkers
.- useFactor
Integer index for which factor to visualize.
- useDimRed
Name of the variable storing dimensionality reduction result in the
cellMeta
slot. Default"UMAP"
.- nLabel
Integer, number of top genes to be shown with text labels. Default
15
.- nPlot
Integer, number of top genes to be shown in the loading rank plot. Default
30
.- ...
Additional plot theme setting arguments passed to
.ggScatter
and.ggplotLigerTheme
.
Examples
result <- getFactorMarkers(pbmcPlot, "ctrl", "stim")
#> ! Factor 7 did not appear as max in any cell in either dataset
#>
plotGeneLoadings(pbmcPlot, result, useFactor = 2)
#> ℹ Plotting feature "Factor_2" on 600 cells
#> ✔ Plotting feature "Factor_2" on 600 cells ... done
#>