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EggHatch.R
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EggHatch.R
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# NOTE TO CONTRIBUTORS: Beyond expanding the functionality of EggHatch there are other potential considerations for its future development. For example:
# we could try and remove as many pacakge dependencies as possible (though this might be quite difficult & ultimately unnecessary);
# we could also imoriove the script below by reducing the number of loops and incorporating piping (i.e., %>%) where possible.
# Object inspection shows that layers are numbered so should be able to access each layer by inputting number also. For example change function
# input to include layer=1(a=4), for example? Maybe a better way to do that? Most sensible way would be to loop through layers and determine
# the index number of the bar for that layer. Removes need for extra input. May need to perform addition or subtraction to values if each layer
# resets index. Investigate.
library(ggplot2)
Example.Data<- data.frame(matrix(vector(), 0, 3, dimnames=list(c(), c("Value", "Variable", "Fill"))), stringsAsFactors=F)
Example.Data[1, ] <- c(80.9, 'Horizontal Pattern','Horizontal Pattern' )
Example.Data[2, ] <- c(67.677777, 'Vertical Pattern','Vertical Pattern' )
Example.Data[3, ] <- c(10.678, 'Mesh HorizVert Pattern','Mesh HorizVert Pattern' )
Example.Data[4,] <- c(95.8, 'Diagonal Pattern 1','Diagonal Pattern 1' )
Example.Data[5,] <- c(67.67, 'Diagonal Pattern 2','Diagonal Pattern 2' )
Example.Data[6,] <- c(58.9, 'Mesh Diagonal Pattern','Mesh Diagonal Pattern' )
Example.Data[7,] <- c(75, 'Mesh HorizVertDiag Pattern','Mesh HorizVertDiag Pattern' )
HighlightDataVert<-Example.Data[2, ]
HighlightHorizontal<-Example.Data[1, ]
HighlightMesh<-Example.Data[3, ]
HighlightHorizontal$Value<-as.numeric(HighlightHorizontal$Value)
Example.Data$Value<-as.numeric(Example.Data$Value)
example_plot<-ggplot(Example.Data, aes(x=Variable, y=Value, fill=factor(Fill))) +
theme_bw() +
theme(legend.position = "none")+
scale_fill_grey(start=.4)+
geom_bar(position='identity', stat="identity", colour="black", width=.86565656)
example_plot
EggHatch <- function(ggplot2_plot, cond.list, width_Man = NULL){
# use this for Relevel
library(Epi)
# default relevel to avoid index issue
ggplot2_plot$data$Variable = Relevel(ggplot2_plot$data$Variable, ref = c(ggplot2_plot$data$Variable))
print("When choosing patterns ensure that scaling does not obscure horizontal lines. Should horizontal lines be obscured consider a different pattern (A, C, D, or any combination of them.)")
# if statement for when no value input in 'fill'
library(stringi)
library(plyr)
library(gtools)
library(stringr)
input_position_dodge<-ggplot2_plot$layers[[1]]$position$width
input_colour<-ggplot2_plot$layers[[1]]$aes_params$colour
fill_value<-ggplot2_plot$layers[[1]]$aes_params$fill
input_size<-ggplot2_plot$theme$rect$size
input_width<-ggplot2_plot$layers[[1]]$geom_params$width
# remove any spaces, tabs etc. from input string
cond.list<-stri_replace_all_charclass(cond.list, "\\p{WHITE_SPACE}", "")
# list of conditions input by users
string_split1<-strsplit(cond.list, ",")[[1]]
# Dataframe shaped to match number of patterns and conditions entries
df <- data.frame(matrix(ncol = 2, nrow = length(string_split1)))
colnames(df) <- c("Pattern", "Condition")
pattern_options <- c("A", "B", "C", "D")
BAR_OUTPUT1<-ggplot2_plot
BAR_OUTPUT<-BAR_OUTPUT1
for (pos in 1:length(string_split1)){
# seperate pattern from input condition into list, dropping '='
cond_patterns <- as.list(strsplit(string_split1[pos], "=")[[1]])
# write values to relevant colomns on current row
df$Pattern[pos]<-cond_patterns[1]
df$Condition[pos]<-cond_patterns[2]
}
# find largest mean value and pass 2% of it
two_percent_of_largest_mean<-((max(unlist(lapply(ggplot2_plot$data$Value,FUN=max)))/100)*2)
# loop around for number of conditions
for (pos in 1:length(df$Condition)){
Condition_Pos=0
# split pattern into individual characters
pattern_split_loop_var<-as.character(df$Pattern[pos])
pattern_split_loop_var<- strsplit(pattern_split_loop_var, "")[[1]]
if(grep("A|B|C|D", df$Pattern[pos], ignore.case=TRUE)){
if ((grepl('A', df$Pattern[pos], ignore.case=TRUE))){
# get 25% of original width
vert_bar_count = (((ggplot2_plot$layers[[1]]$geom_params$width)/100)*10)
Condition_Pos<-as.numeric(df$Condition[pos])
for (i in 1){
if (is.null(fill_value)){
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width=(ggplot2_plot$layers[[1]]$geom_params$width))
}
if (!is.null(fill_value)){
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width=(ggplot2_plot$layers[[1]]$geom_params$width),fill=fill_value)
}
# loop 4 times
for (i in 1:((ggplot2_plot$layers[[1]]$geom_params$width)/vert_bar_count)){
# when calculating the number of times to loop and draw consider making value = bar width
# additionally consider add a verticle line '0' by default. Should get around any
# stepping outside range
# alternative just draw a line on each unit on the x-axis inside bounds of bar: number at given
# point (x-axis label) then either side of number, for example:
# geom_vline(xintercept=c(1.5,2.5, 10.5), linetype="dotted", size=.8)
#
# ensure the Condition_Position value is correct here
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width=(ggplot2_plot$layers[[1]]$geom_params$width)-vert_bar_count, fill='transparent')
vert_bar_count = vert_bar_count + (((ggplot2_plot$layers[[1]]$geom_params$width)/100)*10)#((ggplot2_plot$layers[[1]]$geom_params$width)/4)
}
}
if ((grepl('B', df$Pattern[pos], ignore.case=TRUE))){
point_1_percent_of_current_mean <- ((BAR_OUTPUT$data$Value[Condition_Pos]/100)*.1)
while((BAR_OUTPUT$data$Value[Condition_Pos])>=two_percent_of_largest_mean){
# this breaks while loop to prevent going below x-axis 0
if(((as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-(ggplot2_plot$data$Value[Condition_Pos]/100))<0){
break
}
BAR_OUTPUT$data$Value[Condition_Pos]<-(as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-two_percent_of_largest_mean
# This stops line very close to 0 on y-axis
if(((BAR_OUTPUT$data$Value[Condition_Pos])<((two_percent_of_largest_mean/100)*15))){
break
}
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width, fill='transparent')
}
} # end of sub grepl 'B'
if ((grepl('C', df$Pattern[pos], ignore.case=TRUE))){
# Code for diagonal C
position_input_x<-as.numeric(df$Condition[pos])
position_input_y<-as.numeric(df$Condition[pos])
# half of input width
# when minused from centre of bar point on x-axis
# it gives value at start of bar on x-axis
# inverse true for end of bar width
half_input_width<-input_width/2
ten_perc_input_width<-((input_width/100)*10)
x_axis_min <- position_input_x-half_input_width
x_axis_start_top<-x_axis_min
x_axis_start_bottom<-x_axis_min
x_axis_max <- position_input_x+half_input_width
y_axis_max<- ggplot2_plot$data$Value[position_input_y]
# need to pull the max value from the example_plot the max boundries...
# or caluclate the
z_percent_of_current_mean<-(y_axis_max/100)*10
df_diag <- data.frame(
# start on x-axis-end on x-axis
x = c(x_axis_start_bottom,x_axis_start_top),
# start on y-axis-end on y-axis
y = c(y_axis_max,y_axis_max), Fill='Hope you\'re having a nice day.')
for(i in 1:19){
# run if 2nd x-position is less or equal to rightmost edge of bar
# minus 10% of total input width
if (df_diag$x[2]<(as.character(x_axis_max))){
# 1/10 of unit value in width field
df_diag$x[2]<-df_diag$x[2]+(ten_perc_input_width)
# subtract z percent from 1st y height
df_diag$y[1]<-df_diag$y[1]-(z_percent_of_current_mean)
# draw using current df_diag values
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when less than x_axis_max
# run this code to limit 2nd x-point from moving past rightmost edge of bar
if (df_diag$x[2]==as.character(x_axis_max)){
# drop height of 2nd y-position by z percentage
df_diag$y[2]<-df_diag$y[2]-(z_percent_of_current_mean)
if(df_diag$y[1]<=z_percent_of_current_mean){
df_diag$x[1]<-df_diag$x[1]+ten_perc_input_width
}
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when x_axis_max reached
} # end of for loop 1:19
} # end of sub grepl 'C'
if ((grepl('D', df$Pattern[pos], ignore.case=TRUE))){
# Code for left leaning diagonal 'D'
position_input_x<-as.numeric(df$Condition[pos])
position_input_y<-as.numeric(df$Condition[pos])
# half of input width
# when minused from centre of bar point on x-axis
# it gives value at start of bar on x-axis
# inverse true for end of bar width
half_input_width<-input_width/2
ten_perc_input_width<-((input_width/100)*10)
x_axis_min <- position_input_x-half_input_width
x_axis_max <- position_input_x+half_input_width
y_axis_max<- ggplot2_plot$data$Value[position_input_y]
# need to pull the max value from the example_plot the max boundries...
# or caluclate the
z_percent_of_current_mean<-(y_axis_max/100)*10
df_diag <- data.frame(
# start on x-axis-end on x-axis
x = c(x_axis_max,x_axis_max),
# start on y-axis-end on y-axis
y = c(y_axis_max,y_axis_max), Fill='Hope you\'re having a nice day.')
for(i in 1:19){
# run if 1st x-position is less or equal to leftmost edge of bar
# minus 10% of total input width
if (df_diag$x[2]>(as.character(x_axis_min))){
# 1/10 of unit value in width field
df_diag$x[2]<-df_diag$x[2]-(ten_perc_input_width)
# subtract z percent from 1st y height
df_diag$y[1]<-df_diag$y[1]-(z_percent_of_current_mean)
# draw using current df_diag values
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when less than x_axis_max
# run this code to limit 2nd x-point from moving past rightmost edge of bar
if (df_diag$x[2]==as.character(x_axis_min)){
# drop height of 2nd y-position by z percentage
df_diag$y[2]<-df_diag$y[2]-(z_percent_of_current_mean)
if(df_diag$y[1]<=z_percent_of_current_mean){
df_diag$x[1]<-df_diag$x[1]-ten_perc_input_width
}
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when x_axis_max reached
} # end of for loop 1:19
}
} # end of if grepl 'A'
# This runs code when *only* 'B' in string
if ((!grepl("[^B]", df$Pattern[pos], ignore.case=TRUE))==TRUE){
Condition_Pos<-as.numeric(df$Condition[pos])
one_percent_horiz<-(BAR_OUTPUT$data$Value[Condition_Pos])/100
Twenty_percent_horiz<-(one_percent_horiz*20)
point_1_percent_of_current_mean <- ((BAR_OUTPUT$data$Value[Condition_Pos]/100)*.1)
# draw original bar -> avoids any issue with 'fill' and drawing incorrect height
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width)
# drawing lines (via minusing mean) above 0 on y-axis
while((BAR_OUTPUT$data$Value[Condition_Pos])>=two_percent_of_largest_mean){
# this breaks while loop to prevent going below x-axis 0
if(((as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-(ggplot2_plot$data$Value[Condition_Pos]/100))<0){
break
}
# check null value
if (is.null(fill_value)){
BAR_OUTPUT$data$Value[Condition_Pos]<-(as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-two_percent_of_largest_mean
if(((BAR_OUTPUT$data$Value[Condition_Pos])<((two_percent_of_largest_mean/100)*15))){
break
}
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width)
}
if (!is.null(fill_value)){
BAR_OUTPUT$data$Value[Condition_Pos]<-(as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-two_percent_of_largest_mean
if(((BAR_OUTPUT$data$Value[Condition_Pos])<((two_percent_of_largest_mean/100)*15))){
break
}
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width, fill=fill_value)
}
}
} # end of if grepl 'B'
if ((!grepl('A', df$Pattern[pos], ignore.case=TRUE))==TRUE){
# Only run this code if 'A' is NOT in string - issue lies in BAR_OUTPUT value
if ((grepl('C', df$Pattern[pos], ignore.case=TRUE))){
Condition_Pos<-as.numeric(df$Condition[pos])
if ((grepl('B', df$Pattern[pos], ignore.case=TRUE))){
# draw original bar -> avoids any issue with 'fill' and drawing incorrect height
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width)
point_1_percent_of_current_mean <- ((BAR_OUTPUT$data$Value[Condition_Pos]/100)*.1)
while((BAR_OUTPUT$data$Value[Condition_Pos])>=two_percent_of_largest_mean){
# this breaks while loop to prevent going below x-axis 0
if(((as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-(ggplot2_plot$data$Value[Condition_Pos]/100))<0){
break
}
BAR_OUTPUT$data$Value[Condition_Pos]<-(as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-two_percent_of_largest_mean
# This stops line very close to 0 on y-axis
if(((BAR_OUTPUT$data$Value[Condition_Pos])<((two_percent_of_largest_mean/100)*15))){
break
}
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width, fill='transparent')
}
} # end of sub grepl 'B'
# Code for right leaning diagonal 'C'
position_input_x<-as.numeric(df$Condition[pos])
position_input_y<-as.numeric(df$Condition[pos])
# half of input width
# when minused from centre of bar point on x-axis
# it gives value at start of bar on x-axis
# inverse true for end of bar width
half_input_width<-input_width/2
ten_perc_input_width<-((input_width/100)*10)
x_axis_min <- position_input_x-half_input_width
x_axis_max <- position_input_x+half_input_width
y_axis_max<- ggplot2_plot$data$Value[position_input_y]
# need to pull the max value from the example_plot the max boundries...
# or caluclate the
z_percent_of_current_mean<-(y_axis_max/100)*10
df_diag <- data.frame(
# start on x-axis-end on x-axis
x = c(x_axis_min,x_axis_min),
# start on y-axis-end on y-axis
y = c(y_axis_max,y_axis_max), Fill='Hope you\'re having a nice day.')
for(i in 1:19){
# run if 2nd x-position is less or equal to rightmost edge of bar
# minus 10% of total input width
if (df_diag$x[2]<(as.character(x_axis_max))){
# 1/10 of unit value in width field
df_diag$x[2]<-df_diag$x[2]+(ten_perc_input_width)
# subtract z percent from 1st y height
df_diag$y[1]<-df_diag$y[1]-(z_percent_of_current_mean)
# draw using current df_diag values
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when less than x_axis_max
# run this code to limit 2nd x-point from moving past rightmost edge of bar
if (df_diag$x[2]==as.character(x_axis_max)){
# drop height of 2nd y-position by z percentage
df_diag$y[2]<-df_diag$y[2]-(z_percent_of_current_mean)
if(df_diag$y[1]<=z_percent_of_current_mean){
df_diag$x[1]<-df_diag$x[1]+ten_perc_input_width
}
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when x_axis_max reached
} # end of for loop 1:19
} # end of grepl 'C'
if ((grepl('D', df$Pattern[pos], ignore.case=TRUE))){
Condition_Pos<-as.numeric(df$Condition[pos])
if ((grepl('B', df$Pattern[pos], ignore.case=TRUE))){
# draw original bar -> avoids any issue with 'fill' and drawing incorrect height
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width)
point_1_percent_of_current_mean <- ((BAR_OUTPUT$data$Value[Condition_Pos]/100)*.1)
while((BAR_OUTPUT$data$Value[Condition_Pos])>=two_percent_of_largest_mean){
# this breaks while loop to prevent going below x-axis 0
if(((as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-(ggplot2_plot$data$Value[Condition_Pos]/100))<0){
break
}
BAR_OUTPUT$data$Value[Condition_Pos]<-(as.numeric(BAR_OUTPUT$data$Value[Condition_Pos]))-two_percent_of_largest_mean
# This stops line very close to 0 on y-axis
if(((BAR_OUTPUT$data$Value[Condition_Pos])<((two_percent_of_largest_mean/100)*15))){
break
}
BAR_OUTPUT<-BAR_OUTPUT+geom_bar(data=BAR_OUTPUT$data[Condition_Pos,], position=position_dodge(input_position_dodge), stat="identity", colour=input_colour, size=input_size, width = ggplot2_plot$layers[[1]]$geom_params$width, fill='transparent')
}
} # end of sub grepl 'B'
# Code for left leaning diagonal 'D'
position_input_x<-as.numeric(df$Condition[pos])
position_input_y<-as.numeric(df$Condition[pos])
# half of input width
# when minused from centre of bar point on x-axis
# it gives value at start of bar on x-axis
# inverse true for end of bar width
half_input_width<-input_width/2
ten_perc_input_width<-((input_width/100)*10)
x_axis_min <- position_input_x-half_input_width
x_axis_max <- position_input_x+half_input_width
y_axis_max<- ggplot2_plot$data$Value[position_input_y]
# need to pull the max value from the example_plot the max boundries...
# or caluclate the
z_percent_of_current_mean<-(y_axis_max/100)*10
df_diag <- data.frame(
# start on x-axis-end on x-axis
x = c(x_axis_max,x_axis_max),
# start on y-axis-end on y-axis
y = c(y_axis_max,y_axis_max), Fill='Hope you\'re having a nice day.')
for(i in 1:19){
# run if 1st x-position is less or equal to leftmost edge of bar
# minus 10% of total input width
if (df_diag$x[2]>(as.character(x_axis_min))){
# 1/10 of unit value in width field
df_diag$x[2]<-df_diag$x[2]-(ten_perc_input_width)
# subtract z percent from 1st y height
df_diag$y[1]<-df_diag$y[1]-(z_percent_of_current_mean)
# draw using current df_diag values
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when less than x_axis_max
# run this code to limit 2nd x-point from moving past rightmost edge of bar
if (df_diag$x[2]==as.character(x_axis_min)){
# drop height of 2nd y-position by z percentage
df_diag$y[2]<-df_diag$y[2]-(z_percent_of_current_mean)
if(df_diag$y[1]<=z_percent_of_current_mean){
df_diag$x[1]<-df_diag$x[1]-ten_perc_input_width
}
BAR_OUTPUT<-BAR_OUTPUT+geom_path(data=df_diag, aes(x=x, y=y),colour = "black")
} # end of if statement when x_axis_max reached
} # end of for loop 1:19
} # end of grepl 'D'
} # end of no 'A' if statment
}
} # second loop
BAR_OUTPUT
}
# pattern letters and row numbers
# combine patterns by combining letters, for example: AB, ABC etc.
# A=vertical lines
# B=horizontal lines
# C=diagonal lines bottom-top
# D=diagonal lines top-bottom
# Numbers represent data index (row number) in dataframe
EggHatch_output<-EggHatch(example_plot, ('b=1, A=2, Ba=3, C=4, d=5, Dc=6, ABcD=7'))
EggHatch_output