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Bland & Altman plot

Source: R/Bland_Altman.R
Bland_Altman.Rd

Function to display a Bland & Altman plot in order to visually assess the agreement between CytOpt estimation of the class proportions and the estimate of the class proportions provided through manual gating. Requires that either theta_true or Lab_target was provided when running CytOpT().

Usage

Bland_Altman(proportions, additional_info_shape = NULL)

Arguments

proportions

data.frame of true and estimated proportion returned from CytOpT().

additional_info_shape

vector of additional information to be used for shape in the plot. Not implemented yet.

#'@return a ggplot object

See also

CytOpT

Examples

if(interactive()){

gold_standard_manual_prop <- c(table(HIPC_Stanford_1369_1A_labels) /
 length(HIPC_Stanford_1369_1A_labels))
res <- CytOpT(X_s = HIPC_Stanford_1228_1A, X_t = HIPC_Stanford_1369_1A, 
             Lab_source = HIPC_Stanford_1228_1A_labels,
             theta_true = gold_standard_manual_prop,
             eps = 0.0001, lbd = 0.0001, n_iter = 10000, n_stoc=10,
             step_grad = 10, step = 5, power = 0.99, 
             method='both')
Bland_Altman(res$proportions)

}