vertices
Vector of three unique cluster names that will be used for
plotting. Or a named list that groups clusters as three terminal vertices.
There must not be any overlap between groups.
features
Valid matrix row subsetting index to select features for
similarity calculation. Default NULL
uses all available features.
byCluster
Default NULL
to generate one plot with all cells.
Set "all"
to split cells in plot by cluster and returns a list of
subplots for each cluster as well as the plot including all cells. Otherwise,
a vector of cluster names to generate a list of subplots for the specified
clusters.
veloGraph
Cell x cell dgCMatrix
object containing velocity
information. Shows velocity grid-arrow layer when specified. Default
NULL
does not show velocity.
method
Similarity calculation method. Default "euclidean"
.
Choose from "euclidean"
, "cosine"
, "pearson"
,
"spearman"
.
force
Whether to force calculate the similarity when more then 500
features are detected, which is generally not recommended. Default
FALSE
.
sigma
Gaussian kernel parameter that controls the effect of variance.
Only effective when using a distance metric (i.e. method
is
"euclidian"
or "cosine"
). Larger values tighten the dot
spreading on figure. Default 0.08
.
scale
Whether to min-max scale the distance matrix by clusters.
Default TRUE
.
dotColor
Character vector of color codes. When dotColorBy
is
NULL
, use one or as many colors as the number of cells. If
dotColorBy
is categorical, specify as many colors
as the number of categories in dotColorBy
or ggplot2 categorical
color palette is used by default. If dotColorBy
is continuous, specify
together with breaks
argument.
palette
Color palette to use when dotColorBy
is given. Default
"D"
(viridis) for continuous value and ggplot2 default for categorical
value. See detail for alternatives.
direction
Sets the order of colors in the scale. Default 1
orders as palette default. If -1
, the order of colors is reversed.
breaks
Number of breaks for continuous color scale passed to
non-interactive "plot3D::scatter3D" call. Default NULL
.
returnData
Logical. Whether to return similarity and aggregated
velocity data if applicable instead of generating plot. Default FALSE
.
title
Title text of the plot. Default NULL
.
nGrid
Number of grids along the bottom side of the equilateral
triangle. Default 10
.
radius
Arrow length of unit velocity. Lower this when arrows point
outside of the coordinate. Default 0.1
.
dotSize
Dot aesthetics passed to geom_point
. Default 0.6
when not interactive, 4
when interactive.
dotShuffle
Whether to shuffle the order of dots being added to the
plot, useful when categorical colors are used and mixing of categories is
expected. Default NULL
does shuffle when dotColorBy
given is
categorical and does not otherwise.
labelColors
Colors of the axis lines and vertex labels.
Default c("#3B4992FF", "#EE0000FF", "#008B45FF")
(blue, red and green)
vertexLabelSize
Size of vertex labels. Default 6
when not
interactive, 16
when interactive.
vertexLabelDrift
Position adjustment of the vertex labels, only
applied to non-interactive view. Default 0.03
.
axisBreak
Number of breaks to be labeled along axis. Default
5
.
axisTextShow
Logical, whether to show axis text. Default TRUE
.
axisTextSize
Size of text along each axis break. Default 4
for
non-interactive view, 12
for interactive view.
axisTextDrift
Position adjustment of the axis text, only applied to
non-interactive view. Default 0.01
.
gridLineAlpha
Transparency of background grid lines. Default
0.6
.
arrowLinewidth
Line width of the velocity arrows. Default 0.25
for non-interactive view, 2
for interactive view.
arrowAngle
Controls the angle of the arrowhead, only applied to
non-interactive view. Default 20
.
arrowLen
Control length in centimetre from arrow tip to arrow tail,
only applied to non-interactive view. Default 0.2
.
titleSize
Size of title text. Default 14
for non-interactive
view, 20
for interactive view.
equilateral
Logical, whether to always display the triangle as
equilateral. Default TRUE
.
margin
Margin allowed around of the triangle plotting region when
equilateral = TRUE
interactive
Logical. Whether to display plotly interactive view.
Default FALSE
.