3x3 box and whiskers

reset

set yrange [y1:y2] # where y1 < y2

set xrange [x1:x2] # where x1 < x2

set lmargin 0.5
set bmargin 0.5
set tmargin 0.5
set rmargin 0.5

set boxwidth 0.5 absolute

unset bars

set style fill solid 0.25
set style line 1 lw 3
set grid ytics

set terminal postscript eps enhanced color 'Helvetica' 16 size 5,5

# ==================================
# !!! - Graph for Group_I - DUMMY - !!!
# ==================================

# you gotta run a dummy first because there's some problem with extra tics showing up in the 2nd row of graphs in the first output - this will disappear from subsequent plots generated in the script. This might be glaringly obvious if you want generate more than one cluster of graphs per script.

set output "path/to/Outfile.eps"

set multiplot layout 3,3 scale 1,1 offset 0.5,0.5

set x2tics ("|" x1, "section 1" x1.1, "|" x1.25, "section 2" x1.5, "|" x1.75, "section 3" , "|" x2) font 'Helvetica,11'
set format x ""
set format y
set ylabel "MinorY-1"
set ytics (ytic1,ytic2,ytic3,...,ytic) # where ytic(x) are all some numerical value
plot '/path/to/file/GraphData1.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1 # where x is the column with the x-coordinates and y1<y2<y3<y4<y5
#unset ytics

set format y ""
set ylabel " "
set title "Cluster Title"
plot '/path/to/file/GraphData2.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

set format y ""
set ylabel ""
set title " "
plot '/path/to/file/GraphData3.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

unset x2tics
set format y
set ylabel "MajorY (Major y unit) \n \n MinorY-2"
set ytics (ytic1,ytic2,ytic3,...,ytic) # where ytic(x) are all some numerical value
plot '/path/to/file/GraphData4.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1
#unset ytics

set format y ""
set ylabel ""
plot '/path/to/file/GraphData5.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

plot '/path/to/file/GraphData6.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

#set xtics border in scale 1,0.5 nomirror rotate by +45 offset character 0, 0, 0
set xtics border in scale 1,1 nomirror rotate by +90 offset character 0, -4, 0
set xtics ("xtic1" 1, "xtic2" 2, ..., "xtic" x2)
set format x

set ylabel "MinorY-3"
set xlabel "MinorX-1"
set format y
set ytics (ytic1,ytic2,ytic3,...,ytic) # where ytic(x) are all some numerical value
plot '/path/to/file/GraphData7.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1
#unset ytics

set format y ""
set ylabel ""
set xlabel "MinorX-2"
plot '/path/to/file/GraphData8.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

set xlabel "MinorX-3"
plot '/path/to/file/GraphData9.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

set xlabel ""

unset xtics

unset multiplot

set output

# ==================================
# !!! - Graph for Group_I - ACTUAL - !!!
# ==================================

# you can repeat this as many times as necessary in a single script. The dummy needs to be run only _once_.

set output "path/to/OutfileACTUAL.eps"

set multiplot layout 3,3 scale 1,1 offset 0.5,0.5

set x2tics ("|" x1, "section 1" x1.1, "|" x1.25, "section 2" x1.5, "|" x1.75, "section 3" , "|" x2) font 'Helvetica,11'
set format x ""
set format y
set ylabel "MinorY-1"
set ytics (ytic1,ytic2,ytic3,...,ytic) # where ytic(x) are all some numerical value
plot '/path/to/file/GraphData1.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1
#unset ytics

set format y ""
set ylabel " "
set title "Cluster Title"
plot '/path/to/file/GraphData2.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

set format y ""
set ylabel ""
set title " "
plot '/path/to/file/GraphData3.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

unset x2tics
set format y
set ylabel "MajorY (Major y unit) \n \n MinorY-2"
set ytics (ytic1,ytic2,ytic3,...,ytic) # where ytic(x) are all some numerical value
plot '/path/to/file/GraphData4.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1
#unset ytics

set format y ""
set ylabel ""
plot '/path/to/file/GraphData5.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

plot '/path/to/file/GraphData6.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

#set xtics border in scale 1,0.5 nomirror rotate by +45 offset character 0, 0, 0
set xtics border in scale 1,1 nomirror rotate by +90 offset character 0, -4, 0
set xtics ("xtic1" 1, "xtic2" 2, ..., "xtic" x2)
set format x

set ylabel "MinorY-3"
set xlabel "MinorX-1"
set format y
set ytics (ytic1,ytic2,ytic3,...,ytic) # where ytic(x) are all some numerical value
plot '/path/to/file/GraphData7.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1
#unset ytics

set format y ""
set ylabel ""
set xlabel "MinorX-2"
plot '/path/to/file/GraphData8.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

set xlabel "MinorX-3"
plot '/path/to/file/GraphData9.txt' using x:y2:y1:y5:y4 with candlesticks whiskerbars lt -1 title "", '' using x:y3 with linespoints title "" pt 5 lt -1

set xlabel ""

unset xtics

unset multiplot

set output

set terminal wxt

Percentiles for plotting box and whiskers

# this calculates percentile values and median, then spits out a text file with data. Set to 2.5th ,25th ,50th and 97.5th percentiles.
# it was only recently that i realized that the median is the 50th percentile (right?) and you can just skip the whole "create 2 dataframes and merge before filling in the blank rows" thing by including 0.5 in the by() line above. Following which you just need to fill in any dummy lines necessary.
# the objective here is to produce a dataframe with a _specific_ number of rows (ie: cases). This can be repeated as many times as necessary.
# this is so when you plot it later, all your graphs will have identical x-axis(es?) when you do a big-ass cluster of graphs (see associated gnuplot script)

# Agt.Smith is the name of the dataframe that you wanna use for this. If necessary:
# Agt.Smith <- infile # uncomment if you want to use this, but do i really even have to note this???


Var.Agt.Smith <- data.frame(Agt.Smith$Var,Agt.Smith$CatVar)
colnames(Var.Agt.Smith) <- c("Var","CatVar")
Var.Agt.Smith$CatVar <- factor(Var.Agt.Smith$CatVar)
Var.percentile <- by(Var.Agt.Smith[,1],Var.Agt.Smith$CatVar,quantile,probs=c(0.025, 0.25, 0.75, 0.975),na.rm=T) # change the percentiles as you will.
df1 <- data.frame((matrix(unlist(Var.percentile),nrow=n,byrow=T)),row.names=names(Var.percentile)) # where n is the number of levels in CatVar
colnames(df1) <- c("alpha","bravo","charlie","delta")# these are just generic names for the percentiles calculated above. Feel free to change to something more sensible.
Var.median <- tapply(Var.Agt.Smith$Var,Var.Agt.Smith$CatVar,median,na.rm=T)
df2 <- data.frame(Var.median)
Var.Agt.Smith <- merge(df1,df2,by="row.names")
#blnk.rw <- data.frame(Row.names=c("missing_rowname1","missing_rowname2"),"alpha"=c(NA,NA),bravo=c(NA,NA),charlie=c(NA,NA),delta=c(NA,NA),Var.median=c(NA,NA))# - OPTIONAL - if you need to fill in empty rows
Var.Agt.Smith <- rbind(Var.Agt.Smith,blnk.rw)
Var.Agt.Smith2 <- Var.Agt.Smith[order(Var.Agt.Smith$Row.names),]
Var.Agt.Smith2
Var.Agt.Smith2$dummy.var <- c(1:n) # where n is the number of cases you want
colnames(Var.Agt.Smith2) <- c("#Row.names","alpha","bravo","charlie","delta","Var.median") # at this point, the data frame for the final output willl have 6 columns containing the rownames(which we use to insert dunmy cases into the correct position when necessary), the 4 percentiles, and the median, _in that order_. Feel free to rearrange them in another dataframe if it suits you.
write.table(Var.Agt.Smith2,"path/to/file/Var/Varoutfile.txt",sep="\t",quote=FALSE, row.names=FALSE)

R: Reshaping Data 1 (no calculations)

# this assumes you just want to reshape your data without calculating anything - i couldn't get it to work any other way.
# cast() failed me here, for some reason
# adapted from digithead's lab notebook

# Data input: generic

Var.df <- data.frame(infile$cat.var1,infile$cat.var2,infile$Var)
colnames(Var.df) <- c("CatVar1","CatVar2","Var")

Var <- split(Var.df,Var.df$CatVar2)
result <- data.frame(CatVar1=levels(Var.df$CatVar1))

for (i in seq(along=Var)) { result[[names(Var)[i]]] <- merge(Var[[i]], result, by.x='yymm', all.x=T,all.y=T)$Var}
result

write.table(result,"path/to/output/folder/Var.txt",sep="\t",quote=F,row.names=F)

gnuplot: 3D graphs with 3 diamensional data

# This is a comment. gnuplot will ignore all comments, including this one.
# Stuff in red you gotta change.
# To make the path to the file less messy, you should probably just stick it in the binary folder of your gnuplot directory.
# tested on gnuplot 4.4 for windows

set dgrid3d

set xtics ("label I" 1,"label II" 2, "label III" 3, "label IV" 4, "label V" 5, "label VI" 6, "label VII" 7, "label VIII" 8) # In the same way, you can set ytics and set ztics. Optional.

set xlabel "x label" # Optional.
set ylabel "y label" # Optional.
set zlabel "z label" # Optional.

set xrange [X1:X2] # where X1 < X2. Optional.
set yrange [Y1:Y2] # where Y1 < Y2. Optional.
set zrange [Z1:Z2] # where Z1 < Z2. Optional.

# X is the column where x-coords are
# Y is the column where the y-coords are
# Z1,Z2,Z3 and Z4 are the columns where your variables (those that change with x and y) are.
# the line below is the most important part of this whole script

splot 'file.txt' using X:Y:Z1 with points pt 12 ti "Var A1", \
'file.txt' using X:Y:Z2 with points pt 12 ti "Var A2", \
'file.txt' using X:Y:Z3 with points pt 12 ti "Var A3", \
'file.txt' using X:Y:Z4 with lines ti "Var B" # when it's a 3-d plot, you gotta use splot instead of plot.

R: Redundancy Analysis

# lib(s): vegan

# data input is in the form of a MATRIX.

agt.smith <- as.matrix(infile)

# at minimum:

rda(agt.smith)

# how about some result visualization?

# /* END OF REDUNDANCY ANALYSIS */

R: INDSCAL

# lib(s): SensoMineR

# this particular function was written for the Napping data types i.e. products (stimuli) are positioned on a tableclothe by panelists, then their coordinates are used as input for the Indscal model. I haven't the slightest idea in hell what that means, so if you're equally clueless and gonna go forward with this, well... good luck to you. Fortune favours the brave.

library(SensoMineR)

# data input is in the form of a MATRIX.

agt.smith <- as.matrix(infile)

indscal(agt.smith) # this actually generates some output.

# /* END OF INDSCAL */

R: Biplot (generic)

# I can't get the variables in to a matrix directly. Why? If I knew why, i would fix it. So bear with this.

# put variables of interest into a dataframe:
neo <- data.frame(infile$dep.var1,infile$dep.var2)
agt.smith <- data.frame(infile$indep.var1,infile$indep.var2)

# now put it in a matrix:
x <- as.matrix(neo)
y <- as.matrix(agt.smith)

# and here's the plot:
biplot(x,y)

# for more details: ?biplot

# /* END OF BIPLOTS */