plotFourStates | R Documentation |
Takes four gene sets and visualizes the relative expression of these four gene sets for every barcode by computing it's respective x- and y- coordinates in the state plot. (See details.)
plotFourStates()
Takes the spata-object as the starting point and creates
the necessary data.frame from scratch according to additional parameters.
plotFourStates2()
Takes a data.frame as input.
plotFourStates(
object,
states,
color_by = NULL,
method_gs = NULL,
average_genes = NULL,
pt_alpha = NULL,
pt_clrp = NULL,
pt_clrsp = NULL,
pt_size = NULL,
display_labels = NULL,
verbose = NULL,
of_sample = NA
)
plotFourStates2(
data,
states,
color_by = NULL,
pt_size = 1.5,
pt_alpha = 0.9,
pt_clrsp = "inferno",
pt_clrp = "milo",
display_labels = TRUE
)
object |
An object of class |
states |
The gene sets defining the four states specified as a character vector of length 4. |
color_by |
The variable to be displayed by color:
|
method_gs |
Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to gsva::GSVA(). |
pt_alpha |
Numeric value. Specifies the degree of transparency of all points. |
pt_clrp |
The color palette to be used if the specified variable displayed by
color is categorical/discrete. Run |
pt_clrsp |
The color spectrum to be used if the specified variable displayed by
color is continuous. Run |
pt_size |
Numeric value. Specifies the size of all points. |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
data |
A data.frame containing at least the variables barcodes, |
Returns a ggplot-object that can be additionally customized according to the rules of the ggplot2-framework.
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