Plot 2D embedding
1 2 3 4 5 6 | plotEmbedding(emb, groups = NULL, colors = NULL, cex = 0.6, alpha = 0.4,
gradientPalette = NULL, zlim = NULL, s = 1, v = 0.8,
min.group.size = 1, show.legend = FALSE, mark.clusters = FALSE,
mark.cluster.cex = 2, shuffle.colors = F, legend.x = "topright",
gradient.range.quantile = 0.95, verbose = TRUE,
unclassified.cell.color = "gray70", group.level.colors = NULL, ...)
|
emb |
dataframe with x and y coordinates |
groups |
factor annotations for rows on emb for visualizing cluster annotations |
colors |
color or numeric values for rows on emb for visualizing gene expression |
cex |
point size |
alpha |
point opacity |
gradientPalette |
palette for colors if numeric values provided |
zlim |
range for colors |
s |
saturation of rainbow for group colors |
v |
value of rainbow for group colors |
min.group.size |
minimum size of group in order for group to be colored |
show.legend |
whether to show legend |
mark.clusters |
whether to mark clusters with name of cluster |
mark.cluster.cex |
cluster marker point size |
shuffle.colors |
whether to shuffle group colors |
legend.x |
legend position ie. 'topright', 'topleft', 'bottomleft', 'bottomright' |
gradient.range.quantile |
quantile for mapping colors to gradient palette |
verbose |
verbosity |
unclassified.cell.color |
cells not included in groups will be labeled in this color |
group.level.colors |
set group level colors. Default uses rainbow. |
... |
Additional parameters to pass to BASE::plot |
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