# Plot_HMFA_F.d
#
#' Plot F.d (Group Factor Scores)
#'
#' @param res_HMFA The output of HMFA
#' @param axes Axes to plot
#' @param d Which group to plot
#' @param Flip_axis1 Flag to flip Component 1
#' @param Flip_axis2 Flag to flip Component 2
#' @param dev.new Flag to appease ReporteRs (set FALSE to print results to pptx)
#' @export
Plot_HMFA_F.d <- function(res_HMFA, axes = c(1,2), d = 1, Flip_axis1 = FALSE, Flip_axis2 = FALSE, dev.new = TRUE){
Flip_mat <- makeFlip_mat(Flip_axis1, Flip_axis2)
constraints <- minmaxHelper(mat1 = res_HMFA$res_HMFA$eig$F[,axes] %*% Flip_mat,
mat2 = rbind_array_2_matrix(res_HMFA$res_HMFA$ProjGroup$F[,axes,]) %*% Flip_mat)
alpha <- .8
prettyPlot(res_HMFA$res_HMFA$eig$F[,axes] %*% Flip_mat,
col = add.alpha(res_HMFA$input$DESIGN_rows$colors_AB, alpha),
display_names = F,
constraints = constraints,
cex = 1.25, pch=15, dev.new = dev.new,
main = paste0("Group Factor Scores \nF.(d) for ", res_HMFA$input$DESIGN_tables$labels[d]))
Segments_from_to(From = res_HMFA$res_HMFA$eig$F[,axes] %*% Flip_mat,
To = res_HMFA$res_HMFA$ProjGroup$F[,axes,d] %*% Flip_mat,
XandY = axes,
col = add.alpha(res_HMFA$input$DESIGN_rows$colors_AB, alpha),
lwd = 2)
prettyPlot(res_HMFA$res_HMFA$ProjGroup$F[,axes,d] %*% Flip_mat,
display_names = F,
dev.new = F, new.plot = F,
cex = 2, pch = 16,
col = add.alpha(res_HMFA$input$DESIGN_tables$colors_D[d], alpha))
}
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