#' Creates a sina plot ussing ggplot2 using variables in a metadata (Map) structure
#'
#' The sina plot can represent up to two variables in a single plot
#' @keywords sina
#' @export
#' @examples
#' chibi.sina()
chibi.sina <- function(Map=Map,x_val=NULL,y_val=NULL,col_val=NULL,
mpalette = NULL,facet_formula=NULL,
df_stats = NULL,mean_var = NULL,ymin_var = NULL, ymax_var = NULL,
show_points = TRUE , color_points = FALSE, color_bar = TRUE,
bar_color = "#414141",points_color = "#414141",size_point=10,
alpha_point=0.3,stroke_point=0.5,size_bar=2,width_bar = 0.2,
size_axis_text.x=20,size_axis_text.y=20,
size_axis_title.x=30,size_axis_title.y=30,
size_legend_text=20,size_title_text = 30,strip_text_size=20,legend_proportion_size=2,
size_lines_panel = 0.3,size_panel_border = 1,font_family = "Arial"){
if(is.null(mpalette)){
mpalette <- c("#A6CEE3","#1F78B4","#B2DF8A","#33A02C","#FB9A99","#E31A1C",
"#FDBF6F","#FF7F00","#CAB2D6","#6A3D9A","#FFFF99","#B15928")
#mpalette <- mpalette[1:length(levels(Map[,which(colnames(Map)==col_val)]))]
}
#Evaluate if facet is imposed
if(is.null(facet_formula)){
#No facet
#Compute the statistics for each level on x_val based on y_val
#Evaluate if no dfstats passed
if(is.null(df_stats)){
f1 <- formula(paste0(y_val,"~",x_val))
tdf <- aggregate(f1,Map,
FUN = function(x) c(mmean = mean(x),
mmedian = median(x), msd = sd(x))
)
dfs <- data.frame(Id = tdf[[1]],Mean = tdf[[2]][,1],
Median = tdf[[2]][,2], SD = tdf[[2]][,3])
colnames(dfs)[1] <- x_val
dfs$ymax <- dfs$Mean + dfs$SD
dfs$ymin <- dfs$Mean - dfs$SD
}else{
#Check the names of the xval
if(is.null(mean_var) | is.null(ymin_var) | is.null(ymax_var)){
stop("ERROR: When passing df_stats you should give me the names of the variables with the mean,ymin and ymax",call.=TRUE)
}
#Check if exists the x_val in the passed stats data.frame
if(length(which(colnames(df_stats) == x_val)) == 0){
stop("ERROR: The x_val you chose is not present as column in the df_stats you passed. Please add it",call.=TRUE)
}
dfs <- df_stats
colnames(dfs)[which(colnames(dfs) == mean_var)] <- "Mean"
colnames(dfs)[which(colnames(dfs) == ymin_var)] <- "ymin"
colnames(dfs)[which(colnames(dfs) == ymax_var)] <- "ymax"
#Adjust the levels to be consistent
niv <- levels(Map[,which(colnames(Map) == x_val)])
dfs[,which(colnames(dfs)==x_val)] <- factor(dfs[,which(colnames(dfs) == x_val)],levels = niv)
}
#Here evaluate the different styles
if(show_points == FALSE){
if (color_bar == TRUE){
p <- ggplot(data = Map,aes_string(x = x_val, y = y_val, color = x_val)) +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs, width = width_bar,size = size_bar) +
geom_point(aes(y = Mean), size = size_point, data = dfs)
p <- p + scale_color_manual(values = mpalette)
}else{
p <- ggplot(data = Map,aes_string(x = x_val, y = y_val)) +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs,color = bar_color, width = width_bar,size = size_bar) +
geom_point(aes(y = Mean),color = bar_color, size = size_point, data = dfs)
}
}else{
if(color_points == FALSE & color_bar == TRUE){
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val, color = x_val)) +
geom_sina(size = size_point,shape = 21,alpha = alpha_point, color = points_color) +
geom_point(aes(y = Mean), size = size_point, data = dfs) +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax=ymax),
data = dfs, width = width_bar,size = size_bar)
p <- p + scale_color_manual(values = mpalette)
}else if(color_points == TRUE & color_bar == TRUE){
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val, color = x_val)) +
geom_sina(size = size_point,shape = 21,alpha = alpha_point) +
geom_point(aes(y = Mean), size = size_point, data = dfs) +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs, width = width_bar,size = size_bar)
p <- p + scale_color_manual(values = mpalette)
}else if (color_points == TRUE & color_bar == FALSE){
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val, color = x_val)) +
geom_sina(size = size_point,shape = 21,alpha = alpha_point) +
geom_point(aes(y = Mean), size = size_point, data = dfs,color = bar_color) +
geom_errorbar(aes(y = Mean, ymin = ymin, ymax= ymax),
data = dfs, width = width_bar,size = size_bar,color = bar_color)
p <- p + scale_color_manual(values = mpalette)
}else{
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val)) +
geom_sina(size = size_point,shape = 21,alpha = alpha_point,color = points_color) +
geom_point(aes(y = Mean), size = size_point, data = dfs,color = "#414141") +
geom_errorbar(aes(y = Mean, ymin = ymin, ymax= ymax),
data = dfs, width = width_bar,size = size_bar,color = "#414141")
}
}
}else{
#Facet
facet_formula <- gsub(pattern = " ",replacement = "",x = facet_formula)
lfacet <- length(unlist(strsplit(x = facet_formula,split = "\\+")))
facet_vals <- unlist(strsplit(x = facet_formula,split = "\\+"))
facet_formula <- as.formula(paste("~", facet_formula))
if(lfacet == 1){
#Option of only one facette
#Determine the levels and order of that factor
mlevels <- levels(Map[,which(colnames(Map) == facet_vals[1])])
if(is.null(df_stats)){
f1 <- formula(paste0(y_val,"~",facet_vals[1], "+", x_val))
tdf <- aggregate(f1,Map,
FUN = function(x) c(mmean = mean(x),
mmedian = median(x), msd = sd(x))
)
tdf[,1] <- factor(tdf[,1],levels = mlevels)
#Construct data frame of positions
dfs <- data.frame(Id1 = tdf[[1]],Id2 = tdf[[2]],Mean = tdf[[3]][,1],
Median = tdf[[3]][,2], SD = tdf[[3]][,3])
colnames(dfs)[1:2] <- c(facet_vals[1],x_val)
dfs$ymax <- dfs$Mean + dfs$SD
dfs$ymin <- dfs$Mean - dfs$SD
}else{
if(is.null(mean_var) | is.null(ymin_var) | is.null(ymax_var)){
stop("ERROR: When passing df_stats you should give me the names of the variables with the mean,ymin and ymax",call.=TRUE)
}
#Check if exists the x_val in the passed stats data.frame
if(length(which(colnames(df_stats) == x_val)) == 0){
stop("ERROR: The x_val you chose is not present as column in the df_stats you passed. Please add it",call.=TRUE)
}
#Check if facet vals exist in the structured passed
if(length(which(colnames(df_stats) == facet_vals[1])) == 0){
stop("ERROR: The facet_val you chose is not present as column in the df_stats you passed. Please add it",call.=TRUE)
}
dfs <- df_stats
colnames(dfs)[which(colnames(dfs) == mean_var)] <- "Mean"
colnames(dfs)[which(colnames(dfs) == ymin_var)] <- "ymin"
colnames(dfs)[which(colnames(dfs) == ymax_var)] <- "ymax"
#Adjust the levels to be consistent
niv <- levels(Map[,which(colnames(Map) == x_val)])
dfs[,which(colnames(dfs)==x_val)] <- factor(dfs[,which(colnames(dfs) == x_val)],levels = niv)
niv <- levels(Map[,which(colnames(Map) == facet_vals[1])])
dfs[,which(colnames(dfs)==facet_vals[1])] <- factor(dfs[,which(colnames(dfs) == facet_vals[1])],levels = niv)
}
#Give all the options to construct the sina based on different aesthetics
if(show_points == FALSE){
if (color_bar == TRUE){
p <- ggplot(data = Map,aes_string(x = x_val, y = y_val, color = x_val)) +
facet_grid(facets = facet_formula,scales = "free",space = "free") +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs, width = width_bar,size = size_bar) +
geom_point(aes(y = Mean), size = size_point, data = dfs)
p <- p + scale_color_manual(values = mpalette)
}else{
p <- ggplot(data = Map,aes_string(x = x_val, y = y_val)) +
facet_grid(facets = facet_formula,scales = "free",space = "free") +
geom_errorbar(aes(y = Mean, ymin = ymin, ymax= ymax),
data = dfs,color = bar_color, width = width_bar,size = size_bar) +
geom_point(aes(y = Mean),color = bar_color, size = size_point, data = dfs)
}
}else{
if(color_points == FALSE & color_bar == TRUE){
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val, color = x_val)) +
facet_grid(facets = facet_formula,scales = "free",space = "free") +
geom_sina(size = size_point,shape = 21,alpha = alpha_point, color = points_color) +
geom_point(aes(y = Mean), size = size_point, data = dfs) +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs, width = width_bar,size = size_bar)
p <- p + scale_color_manual(values = mpalette)
}else if(color_points == TRUE & color_bar == TRUE){
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val, color = x_val)) +
facet_grid(facets = facet_formula,scales = "free",space = "free") +
geom_sina(size = size_point,shape = 21,alpha = alpha_point) +
geom_point(aes(y = Mean), size = size_point, data = dfs) +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs, width = width_bar,size = size_bar)
p <- p + scale_color_manual(values = mpalette)
}else if (color_points == TRUE & color_bar == FALSE){
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val, color = x_val)) +
facet_grid(facets = facet_formula,scales = "free",space = "free") +
geom_sina(size = size_point,shape = 21,alpha = alpha_point) +
geom_point(aes(y = Mean), size = size_point, data = dfs,color = bar_color) +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs, width = width_bar,size = size_bar,color = bar_color)
p <- p + scale_color_manual(values = mpalette)
}else{
p <- ggplot(data = Map,aes_string(x = x_val ,y = y_val)) +
facet_grid(facets = facet_formula,scales = "free",space = "free") +
geom_sina(size = size_point,shape = 21,alpha = alpha_point,color = points_color) +
geom_point(aes(y = Mean), size = size_point, data = dfs,color = "#414141") +
geom_errorbar(aes(y = Mean, ymin = ymin , ymax= ymax),
data = dfs, width = width_bar,size = size_bar,color = "#414141")
}
}
}
}
#Add theme to the plot
p <- p + theme(axis.line = element_blank(),
panel.background = element_rect(fill = 'white'),
panel.grid.major.x = element_blank(),
panel.grid.major.y =element_line(colour = "#D9D9D9",size=size_lines_panel),
panel.grid.minor.y = element_line(colour = "#D9D9D9",size=size_lines_panel),
panel.border = element_rect(fill=NA,color = "#414141",size = size_panel_border),
axis.ticks = element_line(colour = "black",size = 2.5),
axis.text.x = element_text(family = font_family,face = "plain",size =size_axis_text.x,colour="#414141",angle = 0),
axis.text.y = element_text(family = font_family,face="plain",size=size_axis_text.y,colour="#414141"),
axis.title.x = element_text(family = font_family,face="plain",size = size_axis_title.x,colour = "#414141"),
axis.title.y = element_text(family = font_family,face="plain",size=size_axis_title.y,colour="#414141"),
legend.background = element_blank(),legend.key.size = unit(legend_proportion_size,"line"),
legend.title=element_text(size=size_title_text,
family = font_family,face = "plain",colour = "#414141"),
legend.key = element_blank(),
legend.text = element_text(size=size_legend_text,family = font_family,face = "plain",colour = "#414141"),
legend.position ="right",strip.text = element_text(family = font_family,colour = "#414141",size = strip_text_size),
strip.background = element_blank())
return(p)
}
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