R/rapt_theme.R

In mkumar-rapttx/RAPTR: Custom R functions for RAPT Therapeutics

#' theme_custom
#'
#' @param base_size
#' @param x_label_size
#' @param y_label_size
#' @param x_tick_label_size
#' @param y_tick_label_size
#' @param y_label_angle Angle to rotate y axis label.
#' @param title_size
#' @param title_just
#' @param legend_position
#'
#' @return
#' @export
#'
theme_custom <- function(base_size = 16,
                         x_label_size = NA, y_label_size = NA,
                         x_tick_label_size = NA, y_tick_label_size = NA,
                         y_label_angle = 90,
                         title_size = NA, title_just = 0.5,
                         legend_position = "top") {
    # Check size inputs
    x_label_size = ifelse(is.na(x_label_size),base_size,x_label_size)
    y_label_size = ifelse(is.na(y_label_size),base_size,y_label_size)
    x_tick_label_size = ifelse(is.na(x_tick_label_size),0.67*base_size,x_tick_label_size)
    y_tick_label_size = ifelse(is.na(y_tick_label_size),0.67*base_size,y_tick_label_size)
    title_size = ifelse(is.na(title_size),base_size,title_size)

    # Modity theme_bw
    theme_bw( base_size = base_size,
	          base_line_size = base_size / 32,
	          base_rect_size = base_size / 32) %+replace%
        theme(
	     # panel.border = element_rect(fill = NA, colour = "grey95")
	      panel.grid = element_line(colour = "grey95"),
	      panel.grid.minor = element_line(size = rel(0.5)),
	      #strip.background = element_rect(fill = "grey90", colour = "grey80"),
	      legend.position = legend_position,
	      legend.background = element_rect(fill = "transparent",color = NA),
	      legend.key = element_rect(fill = "transparent", color = NA),
	      plot.title = element_text(size= title_size, hjust = title_just),
	      panel.background = element_blank(),
	      axis.text.x = element_text(size = x_tick_label_size),
	      axis.text.y = element_text(size = y_tick_label_size),
	      axis.title.x = element_text(size = x_label_size),
	      axis.title.y = element_text(size = y_label_size, angle = y_label_angle)

	    #  complete = TRUE
	    )
}

#' Title
#'
#' @param color
#' @param range
#' @param space
#'
#' @return
#' @export
#'
heatmap_color = function(colors = c("#0A95A7","white","#E5541B"), range = c(-1,0,1), space = "LAB")
{
   return(circlize::colorRamp2(range, colors))
}


#' theme_rapt
#'
#' @param base_size
#' @param x_label_size
#' @param y_label_size
#' @param x_tick_label_size
#' @param y_tick_label_size
#' @param y_label_angle Angle to rotate y axis label.
#' @param title_size
#' @param title_just
#'
#' @return
#' @export
#'
theme_rapt <- function(base_size = 16,
                         x_label_size = NA, y_label_size = NA,
                         x_tick_label_size = NA, y_tick_label_size = NA,
                         y_label_angle = 90,
                         title_size = NA
                         ) {
    # Check size inputs
    x_label_size = ifelse(is.na(x_label_size),base_size,x_label_size)
    y_label_size = ifelse(is.na(y_label_size),base_size,y_label_size)
    x_tick_label_size = ifelse(is.na(x_tick_label_size),0.67*base_size,x_tick_label_size)
    y_tick_label_size = ifelse(is.na(y_tick_label_size),0.67*base_size,y_tick_label_size)
    title_size = ifelse(is.na(title_size),base_size,title_size)

	theme_grey(
		base_size = base_size, base_family = "Source Sans Pro",
		base_line_size = base_size / 22, base_rect_size = base_size / 22
	) %+replace%
	theme(
	  panel.border = element_rect(fill = NA, colour = NA), 
	  panel.grid = element_line(colour = "grey95"),
	  panel.grid.minor = element_line(size = rel(0.5)),
	  strip.background = element_rect(fill = "grey90", colour = "grey80"), 
	  legend.key = element_rect(fill = "white", colour = NA), 
	  plot.title = element_text(size=title_size, hjust = 0, family="Source Serif Pro", margin=unit(c(0,0,1,0),"lines")),
	  axis.text.x = element_text(size = x_tick_label_size),
	  axis.text.y = element_text(size = y_tick_label_size),
	  axis.title.x = element_text(face="bold", margin=unit(c(0.75,0,0,0),"lines"), size=x_label_size),
	  axis.title.y = element_text(face="bold", margin=unit(c(0,0.75,0,0),"lines"), angle=y_label_angle, size = y_label_size),	      
	  panel.background = element_rect(fill = "white", colour = NA),
	  complete = TRUE
		) 
}




#' rapt_extended_colors
#'
#' @return
#' @export
#'
rapt_extended_colors <- function() {	
	c(gray="#5B666F", blue="#0A95A7", orange="#E5541B", yellow="#FE9F33", green="#4DA167", lilac="#947EB0", `dark blue`="#083D77")
}

#' rapt_extended_colors_darker
#'
#' @return
#' @export
#'
rapt_extended_colors_darker <- function() {
	
	c(gray2="#444D54",blue2="#06707E",orange2="#AC3F12",yellow2="#D07920", green2="#356E46", lilac2="#69597D", `dark blue2`="#052344")
}

#rapt_colors <- function(...) {
#	cols <- c(...)
#	full <- c(rapt.extended, rapt.darker.extended)
#	if (is.null(cols)) return(full)
#	return(full[cols])
#}
rapt_pal <- function(palette = "main", reverse = FALSE, ...) {
	if (stringr::str_detect(palette, "dark")) {
		pal <- rapt.darker.extended
	} else if (stringr::str_detect(palette, "both")) {
		pal <-  c(rapt.extended, rapt.darker.extended)
	} else {
		pal <- rapt.extended
	}
	if (reverse) pal <- rev(pal)

	function(n) {
		if (n > length(pal)) stop("Palette ",palette," has a total of ",length(pal)," colors, but you need ",n,"!")
		return(unname(pal)[seq_len(n)])
	}
}

scale_color_rapt <- function(palette="main", reverse = FALSE, ...) {
	pal <- rapt_pal(palette = palette, reverse = reverse)
	discrete_scale("colour", paste0("rapt_", palette), palette = pal, ...)
}
scale_colour_rapt <- scale_color_rapt


scale_fill_rapt <- function(palette = "main", reverse = FALSE, ...) {
	pal <- rapt_pal(palette = palette, reverse = reverse)
	discrete_scale("fill", paste0("rapt_", palette), palette = pal, ...)
}



#
# # data(mtcars)
# # ggplot(mtcars, aes(x=wt, y=drat, color=as.character(cyl))) + geom_point(size=3) + facet_wrap(~cyl) +
# #	theme_rapt() + scale_color_rapt()

theme_manu <- function(base_size = 18){ 
    #font <- "Georgia"   #assign font family up front
    theme_bw(base_size = base_size) %+replace%    #replace elements we want to change
    theme(
      #grid elements
      panel.grid.major.x = element_blank(),    #strip major gridlines
      panel.grid.minor = element_blank(),    #strip minor gridlines
      #axis.ticks = element_blank(),          #strip axis ticks
      
      #text elements
      plot.title = element_text(             #title
                   #family = font,            #set font family
                   size = 20,                #set font size
                   face = 'bold',            #bold typeface
                   hjust = 0.5,                #left align
                   vjust = 2),               #raise slightly
      
      strip.text = element_text(size = 14, face = "bold"),
      strip.background = element_rect(color="white", fill=NA, size=2.5, linetype= "solid")
    )
}