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WaterfallPlotLoader.R
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WaterfallPlotLoader.R
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###########################################################################
# Copyright 2008-2012 Janssen Research & Development, LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
###########################################################################
###########################################################################
#Waterfall Plot
###########################################################################
WaterfallPlot.loader <- function
(
input.filename='outputfile',
concept='',
aggregate.probes = FALSE,
output.file ="Waterfall"
)
{
library(ggplot2)
library(Cairo)
#Pull the data for the histogram.
line.data<-read.delim(input.filename,header=T)
#Order the data by the x column.
line.data <- line.data[order(line.data$X),]
#Add an id column so we can place the boxes on the graph.
line.data$id <- seq_along(line.data$PATIENT_NUM)
#Make the patient_number column numeric.
line.data$PATIENT_NUM <- as.character(line.data$PATIENT_NUM)
#Make the Y axis pretty.
yAxisLabel <- sub(pattern="^\\\\(.*?\\\\){3}",replacement="",x=concept,perl=TRUE)
#Remove spaces from fill column.
line.data$GROUP <- gsub("^\\s+|\\s+$", "",line.data$GROUP)
#Set the fill column factor to have the correct order (follows the scale_fill_manual below).
line.data$GROUP <- factor(line.data$GROUP, levels = c("BASE","LOW","HIGH"))
#Set up the basic plot.
tmp <- ggplot(line.data, aes(PATIENT_NUM,fill=GROUP))
#Add the bars.
tmp <- tmp + geom_rect(aes(x = PATIENT_NUM,ymin = 0, ymax = X,xmin=id - .45, xmax = id + .45))
#Tilt the axis labels.
tmp <- tmp + theme(axis.text.x = element_text(size = 13,angle=90))
#Set the x label.
tmp <- tmp + xlab('Patient Identifier')
#Set the y label.
tmp <- tmp + ylab(yAxisLabel)
#Set the scale color manually.
tmp <- tmp + scale_fill_manual(values = c("black","red","blue"))
CairoPNG(file=paste(output.file,".png",sep=""),width=800,height=800)
print(tmp)
dev.off()
}