Customized version of plotFactors — plotFactors

Modified and optimized version of plotFactors function from LIGER package.

plotFactors_scCustom(
  liger_object,
  num_genes = 8,
  colors_use_factors = NULL,
  colors_use_dimreduc = c("lemonchiffon", "red"),
  pt.size_factors = 1,
  pt.size_dimreduc = 1,
  reduction = "UMAP",
  reduction_label = "UMAP",
  plot_legend = TRUE,
  raster = TRUE,
  raster.dpi = c(512, 512),
  order = FALSE,
  plot_dimreduc = TRUE,
  save_plots = TRUE,
  file_path = NULL,
  file_name = NULL,
  return_plots = FALSE,
  cells.highlight = NULL,
  reorder_datasets = NULL,
  ggplot_default_colors = FALSE,
  color_seed = 123
)

Arguments

liger_object: liger liger_object. Need to perform clustering and factorization before calling this function
num_genes: Number of genes to display for each factor (Default 8).
colors_use_factors: colors to use for plotting factor loadings By default datasets will be plotted using "varibow" with shuffle = TRUE from both from DiscretePalette_scCustomize.
colors_use_dimreduc: colors to use for plotting factor loadings on dimensionality reduction coordinates (tSNE/UMAP). Default is c('lemonchiffon', 'red'),
pt.size_factors: Adjust point size for plotting in the factor plots.
pt.size_dimreduc: Adjust point size for plotting in dimensionality reduction plots.
reduction: Name of dimensionality reduction to use for plotting. Default is "UMAP". Only for newer style liger objects.
reduction_label: What to label the x and y axes of resulting plots. LIGER does not store name of technique and therefore needs to be set manually. Default is "UMAP". Only for older style liger objects.
plot_legend: logical, whether to plot the legend on factor loading plots, default is TRUE. Helpful if number of datasets is large to avoid crowding the plot with legend.
raster: Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.
raster.dpi: Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
order: logical. Whether to plot higher loading cells on top of cells with lower loading values in the dimensionality reduction plots (Default = FALSE).
plot_dimreduc: logical. Whether to plot factor loadings on dimensionality reduction coordinates. Default is TRUE.
save_plots: logical. Whether to save plots. Default is TRUE
file_path: directory file path and/or file name prefix. Defaults to current wd.
file_name: name suffix to append after sample name.
return_plots: logical. Whether or not to return plots to the environment. (Default is FALSE)
cells.highlight: Names of specific cells to highlight in plot (black) (default NULL).
reorder_datasets: New order to plot datasets in for the factor plots if different from current factor level order in cell.data slot. Only for older style liger objects.
ggplot_default_colors: logical. If colors_use_factors = NULL, Whether or not to return plot using default ggplot2 "hue" palette instead of default "varibow" palette.
color_seed: random seed for the palette shuffle if colors_use_factors = NULL. Default = 123.

Value

A list of ggplot/patchwork objects and/or PDF file.

References

Based on plotFactors functionality from original LIGER package.

Author

Velina Kozareva (Original code for modified function), Sam Marsh (Added/modified functionality)

Examples

if (FALSE) {
plotFactors_scCustom(liger_object = liger_obj, return_plots = FALSE, plot_dimreduc = TRUE,
raster = FALSE, save_plots = TRUE)
}