Calculate the signaling velocity of secreted proteins based on their activities.
Usage
SecAct.signaling.velocity.scST(
SpaCET_obj,
sender,
secretedProtein,
receiver,
cellType_meta,
scale.factor = 1e+05,
CustomizedAreaCoordinates = NULL,
radius = 20,
show.coordinates = TRUE,
colors = NULL,
pointSize = 1,
pointAlpha = 1,
legend.position = "right",
legend.size = 1,
arrow.color = "#ff0099",
arrow.width = 1,
arrow.size = 0.3
)Arguments
- SpaCET_obj
A SpaCET object.
- sender
Sender cell types.
- secretedProtein
Secreted proteins.
- receiver
Receiver cell types.
- scale.factor
Sets the scale factor for spot-level normalization.
- CustomizedAreaCoordinates
A vector of four numbers for coordinates of the Customized Area, i.e., x_left, x_right, y_bottom, y_top.
- radius
Radius cut off (unit: um).
- show.coordinates
Whether to show coordinates.
- colors
A vector of colors for spots.
- pointSize
Size of spots.
- pointAlpha
Alpha transparency scales of spots. Must lie between 0 and 1.
- legend.position
The position of the legend. Set it as "none" if you want to remove the legend.
- legend.size
The size of the legend.
- arrow.color
The color of the arrow.
- arrow.width
The width of the arrow.
- arrow.size
The size of the arrow.
Details
The velocity direction starts from the source cell producing a secreted protein and moves to sink cells receiving the secreted protein signal. The velocity magnitude represents the product between the secreted protein-coding gene expression at source cells and signaling activities at sink cells.
Examples
SecAct.signaling.velocity.scST(SpaCET_obj, sender="Fibroblast", secretedProtein="THBS2", receiver="Tumor_boundary", cellType_meta="cellType")
SecAct.signaling.velocity.scST(SpaCET_obj, sender="Fibroblast", secretedProtein="THBS2", receiver="Tumor_boundary", cellType_meta="cellType", CustomizedAreaCoordinates=c(8290,8366,1100,1400))