specificity_plot: Specificity plot

Description

Scatter plot showing specificity of genes as markers for a particular cell subclass. Optimal gene markers for that cell subclass are those genes which are closest to or lie on the y axis, while also being of highest mean expression.

Usage

specificity_plot(
  mk,
  subclass = NULL,
  group = NULL,
  type = 1,
  use_filter = FALSE,
  nrank = 8,
  nsubclass = NULL,
  expfilter = NULL,
  scheme = NULL,
  add_labels = NULL,
  label_pos = "right",
  axis_extend = 0.4,
  nudge_x = NULL,
  nudge_y = NULL,
  ...
)
specificity_plotly(
  mk,
  subclass = NULL,
  group = NULL,
  type = 1,
  use_filter = FALSE,
  nrank = 8,
  nsubclass = NULL,
  expfilter = NULL,
  scheme = NULL,
  ...
)

Value

ggplot2 or plotly scatter plot object.

Arguments

mk: a 'cellMarkers' class object.
subclass: character value specifying the subclass to be plotted.
group: character value specifying cell group to be plotted. One of subclass or group must be specified.
type: Numeric value, either 1 (the default) for a plot of angle on x axis and mean expression on y axis; or 2 for a plot projecting the vector angle into the same plain. See Details below.
use_filter: logical, whether to use gene mean expression to which noise reduction filtering has been applied.
nrank: number of ranks of subclasses to display.
nsubclass: numeric value, number of top markers to label. By default this is obtained from mk for that subclass.
expfilter: numeric value for the expression filter level below which genes are excluded from being markers. Defaults to the level used when cellMarkers() or updateMarkers() was called.
scheme: Vector of colours for points.
add_labels: character vector of additional genes to label
label_pos: character value, either "left" or "right" specifying which side to add labels. Only for type = 1 plots.
axis_extend: numeric value, specifying how far to extend the x axis to the left as a proportion. Only invoked when label_pos = "left".
nudge_x, nudge_y: Label adjustments passed to geom_label_repel() or geom_text_repel().
...: Optional arguments passed to geom_label_repel() or geom_text_repel() for specificity_plot() or plot_ly() for specificity_plotly().

Details

For type = 1, coordinates are drawn as x = angle of vector in degrees, y = mean gene expression of each gene in the subclass of interest. This version is easier to use to identify additional gene markers. The plotly version allows users to hover over points and identify which gene they belong to.

If type = 2, the coordinates are drawn as x = vector length * sin(angle) and y = vector length * cos(angle), where vector length is the Euclidean length of that gene in space where each cell subclass is a dimension. Angle is the angle between the projected vector in space against perfection for that cell subclass, i.e. the vector lying perfectly along the subclass dimension with no deviation along other subclass dimensions, i.e. a gene which is expressed solely in that subclass and has 0 expression in all other subclasses. y is equal to the mean expression of each gene in the subclass of interest. x represents the Euclidean distance of mean expression in all other subclasses, i.e. overall non-specific gene expression in other subclasses. Thus, the plot represents a rotation of all genes as vectors around the axis of the subclass of interest onto the same plane so that the angle with the subclass of interest is visualised between genes.

Colour is used to overlay the ranking of each gene across the subclasses, showing for each gene where the subclass of interest is ranked compared to the other subclasses. Best markers have the subclass of interest ranked 1st.