View source: R/visualization.R
SingleImagePlot | R Documentation |
Single Spatial Plot
SingleImagePlot(
data,
col.by = NA,
col.factor = TRUE,
cols = NULL,
shuffle.cols = FALSE,
size = 0.1,
molecules = NULL,
mols.size = 0.1,
mols.cols = NULL,
mols.alpha = 1,
alpha = molecules %iff% 0.3 %||% 0.6,
border.color = "white",
border.size = NULL,
na.value = "grey50",
dark.background = TRUE,
...
)
data |
A data frame with at least the following columns:
Can pass |
col.by |
Name of column in |
col.factor |
Are the colors a factor or discrete? |
cols |
Colors for cell segmentations; can be one of the following:
|
shuffle.cols |
Randomly shuffle colors when a palette or
vector of colors is provided to |
size |
Point size for cells when plotting centroids |
molecules |
A data frame with spatially-resolved molecule coordinates; should have the following columns:
|
mols.size |
Point size for molecules |
mols.cols |
A vector of color for molecules. The "Set1" palette from RColorBrewer is used by default. |
mols.alpha |
Alpha value for molecules, should be between 0 and 1 |
alpha |
Alpha value, should be between 0 and 1; when plotting multiple
boundaries, |
border.color |
Color of cell segmentation border; pass |
border.size |
Thickness of cell segmentation borders; pass |
na.value |
Color value for |
... |
Ignored |
A ggplot object
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