PlotSpot | R Documentation |
Generate a spot plot for cell-cell interactions similar to the bertin plot. The size or height of the dot or bar represents the interaction strength. The color of the bars and dots represents the p values.
PlotSpot( object, which.cell = NULL, which.gene = NULL, aggregate = c("none", "cell", "gene"), counted = FALSE, selected = FALSE, color = "RdBu", color.bins = 7, type = c("dot", "bar"), order = FALSE, order.dist = "minkowski", p = 1, filter = FALSE, low.cutoff = -Inf, high.cutoff = Inf, dot.scale = 8, plot.y.axis = TRUE, fix.y.axis = TRUE, do.return = FALSE )
object |
Matchmaker object. |
which.cell |
Interacting cell type name (saperated by '|' i.e 'DC|Mac') or index to plot. Default is NULL. |
which.gene |
Interacting gene name (saperated by '_' i.e 'CSF1_CSF1R') or index to plot. Default is NULL. |
aggregate |
Type of aggregation used. Default is none.
|
counted |
Aggregate interactions counts instead of strengths. Default is FALSE. |
selected |
Use selected data if calculated. Default is FALSE. |
color |
Color palette name. Default is "RdBu" (reversed order), high values are in blue and low values in red See details |
color.bins |
Number of differen colors in pallete. Default is 7. See detail |
type |
Types of plot. Default is dotplot.
|
order |
Whether to order the input data. Default is TRUE. See details |
order.dist |
Distance measure to be used. Default is "minkowski". See details |
p |
Power of Minkowski distance Default is 1, aka Manhattan distance. See details |
filter |
Whether to filter the input data based on low.cutoff and high.cutoff. Default is FALSE. |
low.cutoff |
Lower cutoff bound below which will be removed. Default is negative infinity. |
high.cutoff |
Upper cutoff bound above which will be removed. Default is positive infinity. |
dot.scale |
Scale the size of the dots. Default is 8. |
plot.y.axis |
Whether to show y axis for each barplot. Default is TRUE. |
fix.y.axis |
Whether to fix the all barplot ticks or use the relative ticks for each barplot. Default is TRUE. |
do.return |
Whether to return the data used to plot. Default is FALSE. |
A ggplot object or a list with strength and p value data used to generate the plot.
## Not run: PlotSpot(object, which.cell = 1:10, which.gene = 1:10) ## End(Not run)
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