rliger (version 2.2.1)

plotClusterFactorDot: Make dot plot of factor loading in cell groups

Description

This function produces dot plots. Each column represent a group of cells specified by groupBy, each row is a factor specified by useDims. The color of dots reflects mean of factor loading of specified factors in each cell group and sizes reflects the percentage of cells that have loadings of a factor in a group. We utilize ComplexHeatmap for simplified management of adding annotation and slicing subplots. This was inspired by the implementation in scCustomize.

Usage

plotClusterFactorDot(
  object,
  groupBy = NULL,
  useDims = NULL,
  useRaw = FALSE,
  splitBy = NULL,
  factorScaleFunc = NULL,
  cellIdx = NULL,
  legendColorTitle = "Mean Factor\nLoading",
  legendSizeTitle = "Percent\nLoaded",
  viridisOption = "viridis",
  verbose = FALSE,
  ...
)

Value

HeatmapList object.

Arguments

object

A liger object

groupBy

The names of the columns in cellMeta slot storing categorical variables. Loading data would be aggregated basing on these, together with splitBy. Default uses default clusters.

useDims

A Numeric vector to specify exact factors of interests. Default NULL uses all available factors.

useRaw

Whether to use un-aligned cell factor loadings (\(H\) matrices). Default FALSE.

splitBy

The names of the columns in cellMeta slot storing categorical variables. Dotplot panel splitting would be based on these. Default NULL.

factorScaleFunc

A function object applied to factor loading matrix for scaling the value for better visualization. Default NULL.

cellIdx

Valid cell subscription. See subsetLiger. Default NULL for using all cells.

legendColorTitle

Title for colorbar legend. Default "Mean Factor\nLoading".

legendSizeTitle

Title for size legend. Default "Percent\nLoaded"

viridisOption

Name of available viridis palette. See viridis. Default "viridis".

verbose

Logical. Whether to show progress information. Mainly when subsetting data. Default FALSE.

...

Additional theme setting arguments passed to .complexHeatmapDotPlot and heatmap setting arguments passed to Heatmap. See Details.

Details

For ..., please notice that arguments colorMat, sizeMat, featureAnnDF, cellSplitVar, cellLabels and viridisOption from .complexHeatmapDotPlot are already occupied by this function internally. A lot of arguments from Heatmap have also been occupied: matrix, name, heatmap_legend_param, rect_gp, col, layer_fun, km, border, border_gp, column_gap, row_gap, cluster_row_slices, cluster_rows, row_title_gp, row_names_gp, row_split, row_labels, cluster_column_slices, cluster_columns, column_split, column_title_gp, column_title, column_labels, column_names_gp, top_annotation.

Examples

# \donttest{
plotClusterFactorDot(pbmcPlot)
# }