Description Usage Arguments Value
Plots cells according to their coordinates in a dimensionality reduction (tSNE by default,
but also PCA or diffusion map). Cells are colored according to a user set label
that
can range from gene expression, to metadata values, or cluster identity. See
data.for.plot
for more information about labels that can be chosen. Views can
be stored using plotDim3DStoreView
that can reproduce the same orientation
plot repeatedly.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | plotDim3D(
object,
label,
label.type = "search",
reduction.use = c("dm", "pca"),
view = NULL,
dim.1 = NULL,
dim.2 = NULL,
dim.3 = NULL,
w.1 = NULL,
w.2 = NULL,
w.3 = NULL,
cells = NULL,
alpha = 0.2,
size = 4,
title = NULL,
title.cex = 3,
title.line = 0,
bounding.box = T,
xlab = NULL,
ylab = NULL,
zlab = NULL,
continuous.colors = NULL,
continuous.color.limits = NULL,
discrete.colors = NULL
)
|
object |
An URD object |
label |
(Character) Data to use for coloring points (e.g. a metadata name, group ID from clustering, or a gene name) |
label.type |
(Character) Type of data to search for the label. Default is "search" which checks several data types in order. For more information: |
reduction.use |
(Character) Dimensionality reduction to use (Diffusion Map ("dm") or PCA ("pca")) |
view |
(Character) Stored view to use. These are created with |
dim.1 |
(Numeric vector) Component(s) to use on x-axis. If > 1, they will be interpolated according to weights in |
dim.2 |
(Numeric vector) Component(s) to use on y-axis. If > 1, they will be interpolated according to weights in |
dim.3 |
(Numeric vector) Component(s) to use on z-axis. If > 1, they will be interpolated according to weights in |
w.1 |
(Numeric vector) Weight to use for the members of |
w.2 |
(Numeric vector) Weight to use for the members of |
w.3 |
(Numeric vector) Weight to use for the members of |
cells |
(Character vector) Cells to plot. (Default |
alpha |
(Numeric) Transparency of points on plot: 0 (Transparent) - 1 (Opaque) |
size |
(Numeric) Size of points on plot |
title |
(Character) Title for plot. (This is sensitive to resizing the window after plotting, but if a view is stored, the window will be resized before the title is added, so it will be acceptable resolution for figures.) |
title.cex |
(Numeric) Adjust the title font size |
title.line |
(Numeric) Adjust the position of the title. Positive numbers move the title upward. |
bounding.box |
(Logical) Should a bounding box with axis labels be displayed on the plot? |
xlab |
(Character) Label for x-axis (if |
ylab |
(Character) Label for y-axis (if |
zlab |
(Character) Label for z-axis (if |
continuous.colors |
(Character vector) Vector of colors to use if data is continuous |
continuous.color.limits |
(Numeric vector, length 2) Limits of data for color scale. Data outside these limits will be squished. |
discrete.colors |
(Character vector) Vector of colors to use if data is discrete |
Returns nothing, but produces an output through rgl.
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