plotClusterFactorDot: Make dot plot of factor loading in cell groups
In rliger: Linked Inference of Genomic Experimental Relationships

plotClusterFactorDot

R Documentation

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,
  ...
)

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.