plot_feature_rank_single: Feature Rank plot
In Terkild/scfeaturerank: Feature Rank plot for single-cell analysis

Description Usage Arguments Value

View source: R/plot_feature_rank_single.R

Feature Rank plot

plot_feature_rank_single(
  value,
  group = NULL,
  group_color = NULL,
  group_names = NA,
  celltype_group = NULL,
  celltype_group_color = NULL,
  cell_color_by = NULL,
  cell_color = NULL,
  barcode_subsample = 200,
  barplot_group = NULL,
  barplot_stack = NULL,
  barplot_stack_color = NULL,
  barplot_show_total = TRUE,
  barplot_total_fontface = "bold",
  barplot_show_ymax = TRUE,
  barplot_stat_FUN = sum,
  barplot_stat_by = "group",
  barplot_alpha = 1,
  show_density = TRUE,
  show_barplot = TRUE,
  show_barcode = TRUE,
  show_violin = TRUE,
  show_squares = TRUE,
  combine = TRUE,
  ties_method = "first",
  rank_normalize = TRUE,
  threshold_y = NA,
  threshold_color = alpha("black", 0.5),
  threshold_size = 1,
  threshold_linetype = "dashed",
  threshold_show_celltype_pct = TRUE,
  threshold_celltype_pct_fontface = "bold",
  threshold_celltype_pct_size = (theme_get()$text$size/(1/0.352777778)),
  threshold_show_sipk = FALSE,
  threshold_sipk_SD_FUN = scfeaturerank::sd_robust,
  threshold_sipk_denominator = 1000,
  threshold_sipk_size = (theme_get()$text$size/(1/0.352777778)),
  labels = c(),
  ...
)

`value`	Value used for ranking and x-axis (i.e. UMI count).
`group`	Grouping variable for comparison (i.e. titration).
`group_color`	Named vector for coloring groups. Used in density plot.
`group_names`	Rename group levels (i.e. can be used to append concentration or other info that is marker specific)
`celltype_group`	Celltype for grouping cells (i.e. lineage).
`celltype_group_color`	Named vector for coloring celltype_group. Used in violin plot fill.
`cell_color_by`	Variable for coloring cells (i.e. celltype). Used in "barcode" plot.
`cell_color`	Named vector for coloring cells. "Barcode" colors.
`barcode_subsample`	Subsample up to this number of cells from each celltype_group to display in barcode plot
`barplot_group`	Grouping variable for barplots (usually the same as group or celltype_group)
`barplot_stack`	Subgrouping variable for "stacks" within barplot (usually the same as cell_color_by or celltype_group)
`barplot_stack_color`	Named vector for coloring barplot_stack levels
`barplot_show_total`	Should total sums be displayed within barplot? (most meaningful for non-normalized counts)
`barplot_total_fontface`	Font face for total in barplot. Default "bold".
`barplot_show_ymax`	Should maximum y-value tick be shown for barplot? (most meaningful for non-normalized counts)
`barplot_stat_FUN`	Should the barplot show "median" or "sum" (default) of counts?
`barplot_stat_by`	Should stat be normalized to "group" (default) or "none" to show raw value.
`barplot_alpha`	Barplot alpha (can be reduced to make total count more readable)
`show_density`	Should density plot be drawn?
`show_barplot`	Should barplot be drawn?
`show_barcode`	Should barcode plot be drawn?
`show_violin`	Should violin plot be drawn?
`show_squares`	Should group squares above barplot be drawn?
`combine`	Should plot components be combined (default). If FALSE, a list of plot components will be returned.
`ties_method`	ties.method passed on to rank().
`threshold_y`	If not NULL, a threshold line will be drawn at a the set rank. Should be set to expected fraction of positive cells.
`threshold_color`	Threshold line color
`threshold_size`	Threshold line size
`threshold_linetype`	Threshold line type
`threshold_show_celltype_pct`	Show percent above threshold in celltype component
`threshold_celltype_pct_fontface`	Label face for percent above threshold in celltype component
`threshold_celltype_pct_size`	Label size for percent above threshold in celltype component
`threshold_show_sipk`	Should Staining Index Per Thousand (SIPK) be shown in group squares?
`threshold_sipk_SD_FUN`	Function for calculating standard deviation of Staining Index Per Thousand (SIPK). Defaults to scfeaturerank::sd_robust
`threshold_sipk_denominator`	What denominator should be used for value. Defaults to per 1000.
`threshold_sipk_size`	Label size for Staining Index Per Thousand (SIPK).
`labels`	Named vector of axis labels (set element to NULL to remove axis title). Default: c("x.rank"="Value", "y.rank"="Rank", "y.density"="Density", "y.barplot"="Sum")
`...`	Passed on to plot_feature_rank_combine(). Useful for setting relative component sizes.
`rank_normalized`	Should ranks be normalized by group (TRUE) or show as absolute counts (FALSE). Default TRUE.