The function SpaHeatMap is used to visualize the physical location vs cluster or batch.
Usage
SpaHeatMap(
obj,
item = c("cluster", "batch"),
plot_type = c("Scatter", "RGB_TSNE", "RGB_UMAP"),
title_name = NULL,
combine = TRUE,
layout.dim = c(1, 2),
common.legend = TRUE,
...
)
# S3 method for iSCMEBObj
SpaHeatMap(
obj,
item = c("cluster", "batch"),
plot_type = c("Scatter", "RGB_TSNE", "RGB_UMAP"),
title_name = NULL,
combine = TRUE,
layout.dim = c(1, 2),
common.legend = TRUE,
...
)
# S3 method for iSCMEBResObj
SpaHeatMap(
obj,
item = c("cluster", "batch"),
plot_type = c("Scatter", "RGB_TSNE", "RGB_UMAP"),
title_name = NULL,
combine = TRUE,
layout.dim = c(1, 2),
common.legend = TRUE,
...
)
# S3 method for list
SpaHeatMap(
obj,
item = c("cluster", "batch"),
plot_type = c("Scatter", "RGB_TSNE", "RGB_UMAP"),
title_name = NULL,
combine = TRUE,
layout.dim = c(1, 2),
common.legend = TRUE,
...
)Arguments
- obj
A iSCMEBObj object or a iSCMEBResObj object.
- item
Which feature to be used in the plot.
- plot_type
A string shows the type of plot.
- title_name
A string shows the title of plot.
- combine
An indicator of whether plot all on a figure. If TRUE, all figures are plotted; otherwise, return a list with each plot as component. TRUE by default.
- layout.dim
The dimension in the layout of plots when
combine = TRUE.- common.legend
An indicator of whether combine the legend of multiple plots. TRUE by default.
- ...
Arguments passed to other methods.
Value
Return a ggplot2 object or list of ggplots objects.
Return a ggplot2 object or list of ggplots objects.
Return a ggplot2 object or list of ggplots objects.