# HG changeset patch --
Bitbucket.org
# Project galaxy-dist
# URL
http://bitbucket.org/galaxy/galaxy-dist/overview
# User Dan Blankenberg <dan(a)bx.psu.edu>
# Date 1279306372 14400
# Node ID a27244147802bd74be35ae24665cc3fc57580f23
# Parent 11fb3bb5b25058b55d927d4dfb39dab1112f290b
Modify tools contributed by Chungoo Park (cxp440(a)psu.edu) for Linear Discriminant
Analysis, and drawing Receiver Operating Characteristic plots; add a new tool to
'Generate A Matrix for using PC and LDA'; remove redundant 'Principal
Component Analysis' tool.
--- a/test-data/pca_for_lda_output.txt.re_match
+++ /dev/null
@@ -1,87 +0,0 @@
-\"21\.91439361\d*\"
-\"28\.33335569\d*\"
-\"33\.54383183\d*\"
-\"38\.39279966\d*\"
-\"42\.95792886\d*\"
-\"47\.09815550\d*\"
-\"50\.94487376\d*\"
-\"54\.58512629\d*\"
-\"58\.11752456\d*\"
-\"61\.36666878\d*\"
-\"64\.43815007\d*\"
-\"67\.37442210\d*\"
-\"70\.19430653\d*\"
-\"72\.98844264\d*\"
-\"75\.67923231\d*\"
-\"78\.07658354\d*\"
-\"80\.38195983\d*\"
-\"82\.59937656\d*\"
-\"84\.57494344\d*\"
-\"86\.46924307\d*\"
-\"88\.07774382\d*\"
-\"89\.63410862\d*\"
-\"91\.04016474\d*\"
-\"92\.37409738\d*\"
-\"93\.48214466\d*\"
-\"94\.55735875\d*\"
-\"95\.53454224\d*\"
-\"96\.40615879\d*\"
-\"97\.19612900\d*\"
-\"97\.88859479\d*\"
-\"98\.51598802\d*\"
-\"99\.11847048\d*\"
-\"99\.57772251\d*\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
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-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
-\"100\"
--- a/test-data/pca_for_lda_output.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-"21.9143936160079"
-"28.3333556968471"
-"33.5438318357343"
-"38.3927996693607"
-"42.9579288624902"
-"47.0981555066747"
-"50.9448737656701"
-"54.5851262912127"
-"58.117524563425"
-"61.3666687874078"
-"64.4381500783847"
-"67.3744221025279"
-"70.1943065338356"
-"72.9884426407974"
-"75.6792323125723"
-"78.0765835478277"
-"80.381959836786"
-"82.5993765654159"
-"84.5749434452634"
-"86.4692430753353"
-"88.0777438285547"
-"89.6341086298525"
-"91.0401647492736"
-"92.3740973813576"
-"93.4821446651001"
-"94.5573587555456"
-"95.534542246934"
-"96.4061587978985"
-"97.1961290046054"
-"97.888594796593"
-"98.5159880218074"
-"99.11847048736"
-"99.5777225170877"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
-"100"
--- a/tools/stats/plot_from_lda.xml
+++ b/tools/stats/plot_from_lda.xml
@@ -1,24 +1,24 @@
-<tool id="plot_for_lda_output1" name="Draw ROC">
+<tool id="plot_for_lda_output1" name="Draw ROC"
version="1.0.1"><description>Receiver Operating Characteristic
plot</description><command interpreter="sh">r_wrapper.sh
$script_file</command><inputs>
- <param format="text" name="input" type="data"
label="Source file"/>
- <param name="my_title" size="30" type="text"
value="ROC" label="Title of your plot" help="See syntax
below">
- </param>
-
+ <param format="text" name="input" type="data"
label="Source file"></param>
+ <param name="my_title" size="30" type="text"
value="My Figure" label="Title of your plot" help="See syntax
below"></param>
+ <param name="X_axis" size="30" type="text"
value="Text for X axis" label="Legend of X axis in your plot"
help="See syntax below"></param>
+ <param name="Y_axis" size="30" type="text"
value="Text for Y axis" label="Legend of Y axis in your plot"
help="See syntax below"></param></inputs><outputs><data
format="pdf" name="pdf_output" />
- <data format="txt" name="desc_output"
/></outputs><tests><test><param name="input"
value="lda_analy_output.txt"/>
- <param name="my_title" value="Test Plot"/>
+ <param name="my_title" value="Test Plot1"/>
+ <param name="X_axis" value="Test Plot2"/>
+ <param name="Y_axis" value="Test Plot3"/><output
name="pdf_output" file="plot_for_lda_output.pdf"/>
- <output name="desc_output"
file="empty_file.dat"/></test></tests>
@@ -203,7 +203,7 @@
for (i in 1:nfiles) {
r<-rez_ext[[i]]
#tr
- rate<-rbind(rate, c(files_alias[i]," "," "," ") )
+ # rate<-rbind(rate, c(files_alias[i]," "," "," ")
)
mm<-which((r[3,])==max(r[3,]))
m_tr[i]<-mm[1]
@@ -213,9 +213,9 @@
pdf(file= paste("${pdf_output}"))
- plot(rez_ext[[i]][2,]~rez_ext[[i]][3,], xlim=c(0,100), ylim=c(0,100),
xlab="X", ylab="Y", type="l", lty=1, col="blue",
xaxt='n', yaxt='n')
+ plot(rez_ext[[i]][2,]~rez_ext[[i]][3,], xlim=c(0,100), ylim=c(0,100),
xlab="${X_axis} [1-FP(False Positive)]", ylab="${Y_axis} [1-FP(False
Positive)]", type="l", lty=1, col="blue", xaxt='n',
yaxt='n')
for (i in 1:nfiles) {
- lines(rez_ext[[i]][2,]~rez_ext[[i]][3,], xlab="X", ylab="Y",
type="l", lty=1, col=i)
+ lines(rez_ext[[i]][2,]~rez_ext[[i]][3,], xlab="${X_axis} [1-FP(False
Positive)]", ylab="${Y_axis} [1-FP(False Positive)]", type="l",
lty=1, col=i)
# pt=c(r,)
points(x=rez_ext[[i]][3,m_tr[i]],y=rez_ext[[i]][2,m_tr[i]], pch=16, col=i)
}
@@ -236,27 +236,6 @@
<help>
-.. class:: infomark
-
-**What it does**
-
-This tool consists of the module to perform the Linear Discriminant Analysis as described
in Carrel et al., 2006 (PMID: 17009873)
-
-*Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment
Predicts Expression Patterns on the Human Inactive X Chromosome. PLoS Genet 2(9): e151.
doi:10.1371/journal.pgen.0020151*
-
------
-
-**Example**
-
-- Input file
-
- A output file from "LDA" tool is used to perform it.
-
-- Output file
-
- There are two files produced:
- (1) A summary file for LDA classification success rates with optimal tau
- (2) An image file for plot
</help>
Binary file static/images/tools/lda/second_matrix_generator_example_file.png has changed
--- a/test-data/lda_analy_output.txt
+++ b/test-data/lda_analy_output.txt
@@ -1,119 +1,134 @@
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-59.5890410958904, 25, 56.1728395061728, 59.5890410958904, 25,
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+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818,
+81.25, 56.3218390804598, 78.1818181818182, 18.75), .Dim = c(3L,
+201L))
Binary file static/images/tools/lda/first_matrix_generator_example_file.png has changed
Binary file static/images/tools/lda/LDA_Input.png has changed
--- /dev/null
+++ b/tools/stats/generate_matrix_for_pca_lda.xml
@@ -0,0 +1,48 @@
+<tool id="generate_matrix_for_pca_and_lda1" name="Generate A
Matrix">
+ <description>for using PC and LDA</description>
+ <command interpreter="perl">generate_matrix_for_pca_lda.pl $input_1
$input_2 $output</command>
+
+ <inputs>
+ <param format="tabular" name="input_1"
type="data" label="Source file First: a matrix (samples/observations in
rows and variables/features in columns)"></param>
+ <param format="tabular" name="input_2"
type="data" label="Source file Second: a table (samples/observations with
response/class label)"></param>
+ </inputs>
+
+ <outputs>
+ <data format="tabular" name="output" />
+ </outputs>
+
+ <tests>
+ <test>
+ <param name="input_1"
value="matrix_generator_for_pc_and_lda_input_1.tabular"/>
+ <param name="input_2"
value="matrix_generator_for_pc_and_lda_input_2.tabular"/>
+ <output name="output"
file="matrix_generator_for_pc_and_lda_output.tabular"/>
+ </test>
+ </tests>
+
+ <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool consists of a module to generate a matrix to be used for running the Linear
Discriminant Analysis as described in Carrel et al., 2006 (PMID: 17009873)
+
+*Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment
Predicts Expression Patterns on the Human Inactive X Chromosome. PLoS Genet 2(9):
e151. doi:10.1371/journal.pgen.0020151*
+
+-----
+
+**Example**
+
+- Input file (Source file First)
+
+.. image:: ../static/images/tools/lda/first_matrix_generator_example_file.png
+
+
+- Input file (Source file Second)
+
+.. image:: ../static/images/tools/lda/second_matrix_generator_example_file.png
+
+
+</help>
+
+</tool>
--- /dev/null
+++ b/tools/stats/generate_matrix_for_pca_lda.pl
@@ -0,0 +1,147 @@
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+my $Input_Matrix = $ARGV[0];
+my $Input_Label = $ARGV[1];
+
+my %Hash_X = ();
+my %Hash_Y = ();
+my $My_Num_X = 0;
+my $My_Num_Y = 0;
+
+open (OUT, "> $ARGV[2]");
+
+open (LABEL, "< $Input_Label") ||
+ die "Sorry, I couldn't open the escape.txt for clone: $!\n";
+
+my $Label_Index = 0;
+my $X_Label;
+my $input_Label;
+while (defined($input_Label = <LABEL>)){
+ chomp($input_Label);
+ my @cArray_Label = $input_Label =~ /(\S+)\s*/g;
+ if ($input_Label =~ /\w/){
+ if ($Label_Index == 0){
+ $Hash_X{$cArray_Label[0]} = $cArray_Label[1];
+ $X_Label = $cArray_Label[1];
+ $Label_Index = 1;
+ }else{
+ if ($cArray_Label[1] eq $X_Label){
+ $Hash_X{$cArray_Label[0]} = $cArray_Label[1];
+ }else{
+ $Hash_Y{$cArray_Label[0]} = $cArray_Label[1];
+ }
+ }
+ }
+}
+close(LABEL);
+
+open (MATRIX, "< $Input_Matrix") ||
+ die "Sorry, I couldn't open the escape.txt for clone: $!\n";
+
+my %Hash_Matrix = ();
+my %Hash_Features = ();
+my @cArray_Features = ();
+
+my %Hash_Sum = ();
+my $Matrix_Index = 0;
+my $input_Matrix;
+while (defined($input_Matrix = <MATRIX>)){
+ chomp($input_Matrix);
+ my @cArray_Matrix = $input_Matrix =~ /(\S+)\s*/g;
+ if ($input_Matrix =~ /\w/){
+ if ($Matrix_Index == 0){
+ @cArray_Features = @cArray_Matrix;
+ my $Temp_Num_Array = scalar(@cArray_Matrix);
+ my $Temp_Index = 0;
+ for(;$Temp_Index < $Temp_Num_Array; $Temp_Index++){
+ $Hash_Features{$cArray_Matrix[$Temp_Index]} = "BOL";
+ $Hash_Sum{$cArray_Matrix[$Temp_Index]} = 0;
+ }
+ $Matrix_Index = 1;
+ }else{
+ $Hash_Matrix{$cArray_Matrix[0]} = $input_Matrix;
+ }
+ }
+}
+close(MATRIX);
+
+my $Trace_Key;
+
+foreach $Trace_Key (sort {$a cmp $b} keys %Hash_X){
+ my @cArray_Trace_X = $Hash_Matrix{$Trace_Key} =~ /(\S+)\s*/g;
+ my $Num_Array_Feature_X = scalar(@cArray_Features);
+ my $Index_Feature_X = 0;
+ for(;$Index_Feature_X < $Num_Array_Feature_X; $Index_Feature_X++){
+ if ($Hash_Features{$cArray_Features[$Index_Feature_X]} eq "BOL"){
+ $Hash_Features{$cArray_Features[$Index_Feature_X]} = $cArray_Trace_X[$Index_Feature_X
+ 1];
+ }else{
+ $Hash_Features{$cArray_Features[$Index_Feature_X]} =
$Hash_Features{$cArray_Features[$Index_Feature_X]} . "\t" .
$cArray_Trace_X[$Index_Feature_X + 1];
+ }
+
+ $Hash_Sum{$cArray_Features[$Index_Feature_X]} += $cArray_Trace_X[$Index_Feature_X +
1];
+ }
+ $My_Num_X ++;
+}
+
+my $Append_Key;
+foreach $Append_Key (keys %Hash_Features){
+ $Hash_Features{$Append_Key} = $Hash_Features{$Append_Key} . "\t" .
$Hash_Sum{$Append_Key};
+ $Hash_Sum{$Append_Key} = 0;
+}
+
+foreach $Trace_Key (sort {$a cmp $b} keys %Hash_Y){
+ my @cArray_Trace_Y = $Hash_Matrix{$Trace_Key} =~ /(\S+)\s*/g;
+ my $Num_Array_Feature_Y = scalar(@cArray_Features);
+ my $Index_Feature_Y = 0;
+ for(;$Index_Feature_Y < $Num_Array_Feature_Y; $Index_Feature_Y++){
+ if ($Hash_Features{$cArray_Features[$Index_Feature_Y]} eq "BOL"){
+ $Hash_Features{$cArray_Features[$Index_Feature_Y]} = $cArray_Trace_Y[$Index_Feature_Y
+ 1];
+ }else{
+ $Hash_Features{$cArray_Features[$Index_Feature_Y]} =
$Hash_Features{$cArray_Features[$Index_Feature_Y]} . "\t" .
$cArray_Trace_Y[$Index_Feature_Y + 1];
+ }
+
+ $Hash_Sum{$cArray_Features[$Index_Feature_Y]} += $cArray_Trace_Y[$Index_Feature_Y +
1];
+ }
+ $My_Num_Y ++;
+}
+
+foreach $Append_Key (keys %Hash_Features){
+ $Hash_Features{$Append_Key} = $Hash_Features{$Append_Key} . "\t" .
$Hash_Sum{$Append_Key} . "\t" . "EOL";
+}
+
+my $Prt_Key;
+print OUT " \t";
+foreach $Prt_Key (sort {$a cmp $b} keys %Hash_X){
+ print OUT "$Prt_Key \t";
+}
+print OUT "X(SUM) \t";
+
+foreach $Prt_Key (sort {$a cmp $b} keys %Hash_Y){
+ print OUT "$Prt_Key \t";
+}
+print OUT "Y(SUM) \t";
+print OUT "\n";
+
+my $Prt_Index = 0;
+my $Prt_Array_Num = scalar (@cArray_Features);
+for(;$Prt_Index < $Prt_Array_Num; $Prt_Index++){
+ print OUT "$cArray_Features[$Prt_Index]
\t$Hash_Features{$cArray_Features[$Prt_Index]}\n";
+}
+
+print OUT " \t";
+my $My_Label_Index = 0;
+for(;$My_Label_Index < $My_Num_X; $My_Label_Index++){
+ print OUT "X \t";
+}
+print OUT " \t";
+
+$My_Label_Index = 0;
+for(;$My_Label_Index < $My_Num_Y; $My_Label_Index++){
+ print OUT "Y \t";
+}
+print OUT " \t\n";
+
+close(OUT);
--- a/tools/stats/pca_for_lda.xml
+++ /dev/null
@@ -1,245 +0,0 @@
-<tool id="pca_for_lda1" name="Calculate PC">
- <description>Principal Component Analysis</description>
- <command interpreter="sh">r_wrapper.sh $script_file</command>
-
- <inputs>
- <param format="tabular" name="input" type="data"
label="Source file">
- </param>
- </inputs>
-
- <outputs>
- <data format="txt" name="output" />
- </outputs>
-
- <tests>
- <test>
- <param name="input"
value="pca_and_lda_analy_for_lda_input.tabular"/>
- <output name="output"
file="pca_for_lda_output.txt.re_match" compare="re_match"/>
- </test>
- </tests>
-
- <configfiles>
- <configfile name="script_file">
-
- rm(list = objects() )
-
- ############# FORMAT X DATA #########################
- format<-function(data) {
- ind=NULL
- for(i in 1 : ncol(data)){
- if (is.na(data[nrow(data),i])) {
- ind<-c(ind,i)
- }
- }
- #print(is.null(ind))
- if (!is.null(ind)) {
- data<-data[,-c(ind)]
- }
-
- data
- }
-
- ########GET RESPONSES ###############################
- get_resp<- function(data) {
- resp1<-as.vector(data[,ncol(data)])
- resp=numeric(length(resp1))
- for (i in 1:length(resp1)) {
- if (resp1[i]=="Control ") {
- resp[i] = 0
- }
- if (resp1[i]=="XLMR ") {
- resp[i] = 1
- }
- }
- return(resp)
- }
-
- ######## CHARS TO NUMBERS ###########################
- f_to_numbers<- function(F) {
- ind<-NULL
- G<-matrix(0,nrow(F), ncol(F))
- for (i in 1:nrow(F)) {
- for (j in 1:ncol(F)) {
- G[i,j]<-as.integer(F[i,j])
- }
- }
- return(G)
- }
-
- ###################NORMALIZING#########################
- norm <- function(M, a=NULL, b=NULL) {
- C<-NULL
- ind<-NULL
-
- for (i in 1: ncol(M)) {
- if (sd(M[,i])!=0) {
- M[,i]<-(M[,i]-mean(M[,i]))/sd(M[,i])
- }
- # else {print(mean(M[,i]))}
- }
- return(M)
- }
-
- ##### LDA DIRECTIONS #################################
- lda_dec <- function(data, k){
- priors=numeric(k)
- grandmean<-numeric(ncol(data)-1)
- means=matrix(0,k,ncol(data)-1)
- B = matrix(0, ncol(data)-1, ncol(data)-1)
- N=nrow(data)
- for (i in 1:k){
- priors[i]=sum(data[,1]==i)/N
- grp=subset(data,data\$group==i)
- means[i,]=mean(grp[,2:ncol(data)])
- #print(means[i,])
- #print(priors[i])
- #print(priors[i]*means[i,])
- grandmean = priors[i]*means[i,] + grandmean
- }
-
- for (i in 1:k) {
- B= B + priors[i]*((means[i,]-grandmean)%*%t(means[i,]-grandmean))
- }
-
- W = var(data[,2:ncol(data)])
- svdW = svd(W)
- inv_sqrtW =solve(svdW\$v %*% diag(sqrt(svdW\$d)) %*% t(svdW\$v))
- B_star= t(inv_sqrtW)%*%B%*%inv_sqrtW
- B_star_decomp = svd(B_star)
- directions = inv_sqrtW%*%B_star_decomp\$v
- return( list(directions, B_star_decomp\$d) )
- }
-
- ################ NAIVE BAYES FOR 1D SIR OR LDA ##############
- naive_bayes_classifier <- function(resp, tr_data, test_data, k=2, tau) {
- tr_data=data.frame(resp=resp, dir=tr_data)
- means=numeric(k)
- #print(k)
- cl=numeric(k)
- predclass=numeric(length(test_data))
- for (i in 1:k) {
- grp = subset(tr_data, resp==i)
- means[i] = mean(grp\$dir)
- #print(i, means[i])
- }
- cutoff = tau*means[1]+(1-tau)*means[2]
- #print(tau)
- #print(means)
- #print(cutoff)
- if (cutoff>means[1]) {
- cl[1]=1
- cl[2]=2
- }
- else {
- cl[1]=2
- cl[2]=1
- }
-
- for (i in 1:length(test_data)) {
-
- if (test_data[i] <= cutoff) {
- predclass[i] = cl[1]
- }
- else {
- predclass[i] = cl[2]
- }
- }
- #print(means)
- #print(mean(means))
- #X11()
- #plot(test_data,pch=predclass, col=resp)
- predclass
- }
-
- ################# EXTENDED ERROR RATES #################
- ext_error_rate <- function(predclass, actualclass,msg=c("you forgot
the message"), pr=1) {
- er=sum(predclass != actualclass)/length(predclass)
-
- matr<-data.frame(predclass=predclass,actualclass=actualclass)
- escapes = subset(matr, actualclass==1)
- subjects = subset(matr, actualclass==2)
- er_esc=sum(escapes\$predclass !=
escapes\$actualclass)/length(escapes\$predclass)
- er_subj=sum(subjects\$predclass !=
subjects\$actualclass)/length(subjects\$predclass)
-
- if (pr==1) {
- # print(paste(c(msg, 'overall : ', (1-er)*100,
"%."),collapse=" "))
- # print(paste(c(msg, 'within escapes : ', (1-er_esc)*100,
"%."),collapse=" "))
- # print(paste(c(msg, 'within subjects: ', (1-er_subj)*100,
"%."),collapse=" "))
- }
- return(c((1-er)*100, (1-er_esc)*100, (1-er_subj)*100))
- }
-
- ## Main Function ##
-
- files<-matrix("${input}", 1,1, byrow=T)
-
- tau<-seq(0,1, by=0.005)
- #tau<-seq(0,1, by=0.1)
- for_curve=matrix(-10, 3,length(tau))
-
- ##############################################################
-
- test_data_whole_X <-read.delim(files[1,1], row.names=1)
-
- #### FORMAT TRAINING DATA ####################################
- # get only necessary columns
-
- test_data_whole_X<-format(test_data_whole_X)
-
oligo_labels<-test_data_whole_X[1:(nrow(test_data_whole_X)-1),ncol(test_data_whole_X)]
- test_data_whole_X<-test_data_whole_X[,1:(ncol(test_data_whole_X)-1)]
-
- X_names<-colnames(test_data_whole_X)[1:ncol(test_data_whole_X)]
- test_data_whole_X<-t(test_data_whole_X)
- resp<-get_resp(test_data_whole_X)
- ldaqda_resp = resp + 1
- a<-sum(resp) # Number of Subject
- b<-length(resp) - a # Number of Escape
- ## FREQUENCIES #################################################
- F<-test_data_whole_X[,1:(ncol(test_data_whole_X)-1)]
- F<-f_to_numbers(F)
- FN<-norm(F, a, b)
- ss<-svd(FN)
- eigvar<-NULL
- eig<-ss\$d^2
-
- print_out <- c(rep('NA', length(ss\$d)))
- for ( i in 1:length(ss\$d)) {
- eigvar[i]<-sum(eig[1:i])/sum(eig)
- # print(paste(c("Variance explained : ", eigvar[i]*100, "
%"), collapse=""))
- print_out[i] <- c(eigvar[i]*100)
- }
-
- #My_Names <- c("order of principal components",
"accumulated variance explained", "")
- #names(print_out)<-My_Names
-
- write.table(print_out, file = "${output}", col.names = FALSE, row.names
= FALSE)
-
- </configfile>
- </configfiles>
-
- <help>
-
-.. class:: infomark
-
-**What it does**
-
-This tool consists of the first module to perform the Principal Component Analysis as
described in Carrel et al., 2006 (PMID: 17009873)
-
-*Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment
Predicts Expression Patterns on the Human Inactive X Chromosome. PLoS Genet 2(9):
e151. doi:10.1371/journal.pgen.0020151*
-
------
-
-**Example**
-
-- Input file
-
-.. image:: ../static/images/tools/lda/LDA_Input.png
-
-- Output file
-
- The values indicate "accumulated variance explained (%)" and were sorted by
the order of principal components (i.e., 1st, 2nd, 3rd, 4th...).
-
-
-</help>
-
-</tool>
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -129,7 +129,7 @@
<tool file="stats/gsummary.xml" /><tool
file="filters/uniq.xml" /><tool file="stats/cor.xml" />
- <tool file="stats/pca_for_lda.xml" />
+ <tool file="stats/generate_matrix_for_pca_lda.xml" /><tool
file="stats/lda_analy.xml" /><tool
file="stats/plot_from_lda.xml" /><tool
file="regVariation/t_test_two_samples.xml" />
--- /dev/null
+++ b/test-data/matrix_generator_for_pc_and_lda_input_1.tabular
@@ -0,0 +1,88 @@
+ CTCAGAAAAAAA CCATCCATCCATCCATCC AGAGGGAGAGGG ATCTGTTGATGG AGGGGTGACAGA ATCCCATTTACA
AAGGGTATCAGT ATAATATATACA TATTATATGTATA CATCATCATCATCA CCCCATGATCCA TGATTCCTTAAAGAA
AACACTTGGACA TATTAATATAATTTATAAA ATGTTTATTTTA TATCCAGGAGAA CAATTCTCCTGCC
ACCATAAAAATGAGAAC CTCAGCCATAAAAA ATGAGTGAGAATAT ACTGTGAGTCAA
TAAACTAAAGAGCTTCTGCACAGCA TCCTTTGGGTATAT ATGCTGCTATAAAGACACATGCACAC
TGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTG TCCACAATGGTTGAA TTGGCTGCATAAAT
CAATGGAACAGAACAGAGCCCTCAGAAATAA GAACTAGAAATACCATTTGACCCAGC TCAAAGATCAGAT
GACCCATCTCACACCAGTTAGAATG CAAAGAGAATAAAATACCTAGGTATTTTATTCTTTTT AAAATGGCCATACTGCCCAAG
AAATTTTTCCAATTCTGTGAAGAAA TTCACAATAGCAAAGAC TAGGAAGAATCAATA CTGGGTATATACCCAGTAATGG
TTGGAAGTTCTGGCCAGGGCAA TGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAA
CTCTCACCACTCCTATTCAACATA ACACACACATAT CCATGAGCATGGAATGTTCT AACCCAAATGTCC
TTTACAAGAAAAAAACAAACAACCCCA AGTTCTAGATCC CTGGAAGCATTCCCTTT GATCCCATTTGTC
GATATGAACAGACA TGGGTTTGTCATA AGTTTCTTTTGC A
ATTACCCAGTCT TCATGTCATCTGCAAACA AAAACTCTCAAT CAACTTCAGCAA ATTGGCTGTGGGTTT
AATTAGATCCCA GACCTAAAACCA AGAATCTACAAT AAACCAAACACC GGAGTTCCAGACCAGCCT CCTTGCCCATGCC
ATCATACTGAAT AGGAAGTCAAATT AGCAAACCACCA AGCATGATTTATA GAGAGCCAAATCATGAGTG
AAAGAGCCAAAT AGCAATTGTGAATGG CACTATTCACAATTGC TCAGGATACAAAATCAATG CAATGAACTCAAACAAATT
TCCAACAAAGGACATGAACTCATC AATTGAACAATGAGAACATGTGGTAT AACCACAATGAGAACA GTGTATATATATACAT
ACATATATATAT GTCAGATGGATA TCATCTGACAAAGGGCTAATATCCAG TTTGTCAGGTTTGTCAAAG
TTCTTAATCCAGTCTATCATT TTTAATCCATCTTGA AAACTACCATCAGAGTGAACAGGCA GCCATCAGAGAAAT
ACAGGCAACCTACA GCAACCTACTCA TAGAAAACCCCAT
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--- a/tools/stats/lda_analy.xml
+++ b/tools/stats/lda_analy.xml
@@ -1,9 +1,9 @@
-<tool id="lda_analy1" name="Perform LDA">
+<tool id="lda_analy1" name="Perform LDA"
version="1.0.1"><description>Linear Discriminant
Analysis</description><command interpreter="sh">r_wrapper.sh
$script_file</command><inputs><param format="tabular"
name="input" type="data" label="Source file"/>
- <param name="cond" size="30" type="integer"
value="3" label="Number of principal components" help="See syntax
below">
+ <param name="cond" size="30" type="integer"
value="3" label="Number of principal components" help="See TIP
below"><validator type="empty_field" message="Enter a valid
number of principal components, see syntax below for examples"/></param>
@@ -14,7 +14,7 @@
<tests><test>
- <param name="input"
value="pca_and_lda_analy_for_lda_input.tabular"/>
+ <param name="input"
value="matrix_generator_for_pc_and_lda_output.tabular"/><output
name="output" file="lda_analy_output.txt"/><param
name="cond" value="2"/>
@@ -47,10 +47,10 @@
resp1<-as.vector(data[,ncol(data)])
resp=numeric(length(resp1))
for (i in 1:length(resp1)) {
- if (resp1[i]=="Control ") {
+ if (resp1[i]=="Y ") {
resp[i] = 0
}
- if (resp1[i]=="XLMR ") {
+ if (resp1[i]=="X ") {
resp[i] = 1
}
}
@@ -256,6 +256,12 @@
<help>
+.. class:: infomark
+
+**TIP:** If you want to perform Principal Component Analysis (PCA) on the give numeric
input data (which corresponds to the "Source file First in "Generate A
Matrix" tool), please use *Multivariate Analysis/Principal Component Analysis*
+
+-----
+
.. class:: infomark
**What it does**
@@ -266,16 +272,13 @@ This tool consists of the module to perf
-----
-**Example**
+.. class:: warningmark
-- Input file
+**Note**
-.. image:: ../static/images/tools/lda/LDA_Input.png
+- Output from "Generate A Matrix" tool is used as input file for this tool
+- Output of this tool contains LDA classification success rates for different values of
the turning parameter tau (from 0 to 1 with 0.005 interval). This output file will be used
to establish the ROC plot, and you can obtain more detail information from this plot.
-- Output file
-
- LDA classification success rates for different values of the turning parameter tau (from
0 to 1 with 0.005 interval).
- This output file will be used to establish the ROC plot.
</help>
--- /dev/null
+++ b/test-data/matrix_generator_for_pc_and_lda_output.tabular
@@ -0,0 +1,88 @@
+ AGTR2 ARHGEF9 BRWD3 CLCN5 FMR1 GPC3 GPR173 GRIA3 GSPT2 HUWE1 KIAA2022 KLF8
MAGEH1 MTM1 NUDT10 NUDT11 PAGE1 PAGE4 PAK3 PCSK1N PGK1 PHF6 RRAGB SHROOM4
SOX3 TMEM29 TRO TSR2 USP51 UXT ZDHHC15 ZDHHC9 X(SUM) APOOL AR BEX4 BEX5
CHIC1 CHM CPXCR1 CSTF2 CXCR3 CXorf26 CYSLTR1 DACH2 DIAPH2 DRP2 EDA ESX1 FGF16
FXYD8 GPR23 HDX HEPH IL1RAPL2 ITM2A KIAA1166 KLHL4 LAS1L MAGEE1 MAGEE2 MSN
MTMR8 NAP1L2 NRK NSBP1 NXF3 P2RY10 PABPC5 POF1B RNF12 RPS6KA6 SLC7A3 SPIN2A
SPIN3 SPIN4 STARD8 SYTL4 TAF9B TBX22 TCEAL2 TCEAL4 TMEM28 UBQLN2 UPRT ZCCHC5
ZNF711 ZXDA Y(SUM)
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+GGAGTTCCAGACCAGCCT
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+TAGAAAACCCCAT
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+ X X X X X X X X X X X X X X X X X X X X X X X X X X X X X
X X X Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
--- a/test-data/plot_for_lda_output.pdf
+++ b/test-data/plot_for_lda_output.pdf
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--- /dev/null
+++ b/test-data/matrix_generator_for_pc_and_lda_input_2.tabular
@@ -0,0 +1,87 @@
+ARHGEF9 XLMR
+KIAA2022 XLMR
+ZDHHC15 XLMR
+PGK1 XLMR
+BRWD3 XLMR
+PAK3 XLMR
+AGTR2 XLMR
+GRIA3 XLMR
+ZDHHC9 XLMR
+GPC3 XLMR
+PHF6 XLMR
+SOX3 XLMR
+FMR1 XLMR
+MTM1 XLMR
+SHROOM4 XLMR
+KLF8 XLMR
+UXT XLMR
+PCSK1N XLMR
+PAGE1 XLMR
+PAGE4 XLMR
+CLCN5 XLMR
+NUDT10 XLMR
+NUDT11 XLMR
+GSPT2 XLMR
+TMEM29 XLMR
+GPR173 XLMR
+HUWE1 XLMR
+TSR2 XLMR
+TRO XLMR
+MAGEH1 XLMR
+USP51 XLMR
+RRAGB XLMR
+UBQLN2 CONTROL
+SPIN3 CONTROL
+SPIN2A CONTROL
+ZXDA CONTROL
+SPIN4 CONTROL
+MTMR8 CONTROL
+KIAA1166 CONTROL
+LAS1L CONTROL
+MSN CONTROL
+HEPH CONTROL
+AR CONTROL
+STARD8 CONTROL
+TMEM28 CONTROL
+EDA CONTROL
+SLC7A3 CONTROL
+CXCR3 CONTROL
+NAP1L2 CONTROL
+CHIC1 CONTROL
+FXYD8 CONTROL
+RNF12 CONTROL
+UPRT CONTROL
+MAGEE2 CONTROL
+CXorf26 CONTROL
+MAGEE1 CONTROL
+FGF16 CONTROL
+TAF9B CONTROL
+CYSLTR1 CONTROL
+ZCCHC5 CONTROL
+GPR23 CONTROL
+P2RY10 CONTROL
+ITM2A CONTROL
+TBX22 CONTROL
+NSBP1 CONTROL
+RPS6KA6 CONTROL
+HDX CONTROL
+APOOL CONTROL
+ZNF711 CONTROL
+POF1B CONTROL
+CHM CONTROL
+DACH2 CONTROL
+KLHL4 CONTROL
+CPXCR1 CONTROL
+PABPC5 CONTROL
+DIAPH2 CONTROL
+SYTL4 CONTROL
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--- a/test-data/pca_and_lda_analy_for_lda_input.tabular
+++ /dev/null
@@ -1,89 +0,0 @@
- ARHGEF9 KIAA2022 ZDHHC15 PGK1 BRWD3 PAK3 AGTR2 GRIA3 ZDHHC9 GPC3 PHF6 SOX3
FMR1 MTM1 SHROOM4 KLF8 Sum(XLMR) UXT PCSK1N PAGE1 PAGE4 CLCN5 NUDT10 NUDT11
GSPT2 TMEM29 GPR173 HUWE1 TSR2 TRO MAGEH1 USP51 RRAGB UBQLN2 SPIN3 SPIN2A
ZXDA SPIN4 MTMR8 KIAA1166 LAS1L MSN HEPH AR STARD8 TMEM28 EDA SLC7A3 CXCR3
NAP1L2 CHIC1 FXYD8 RNF12 UPRT MAGEE2 CXorf26 MAGEE1 FGF16 TAF9B CYSLTR1 ZCCHC5
GPR23 P2RY10 ITM2A TBX22 NSBP1 RPS6KA6 HDX APOOL ZNF711 POF1B CHM DACH2 KLHL4
CPXCR1 PABPC5 DIAPH2 SYTL4 CSTF2 DRP2 TCEAL2 BEX5 NXF3 BEX4 TCEAL4 ESX1
IL1RAPL2 NRK SERPINA7 MUM1L1 CXorf57 MORC4 VSIG1 NXT2 TMEM164 CHRDL1 PAK3
ZCCHC16 LRCH2 LUZP4 PLS3 AGTR2 CXorf61 KLHL13 WDR44 LONRF3 PGRMC1 SLC25A43
6-Sep NKAP ZBTB33 FAM70A ATP1B4 C1GALT1C1 GLUD2 GRIA3 THOC2 SH2D1A ODZ1 WDR40C
ACTRT1 APLN XPNPEP2 UTP14A BCORL1 ENOX2 FLJ30058 MST4 RAP2C MBNL3 HS6ST2 GPC4
PHF6 DDX26B FHL1
BRS3 ZIC3 FGF13 F9 CDR1 SPANXB1 LDOC1 SPANXE MAGEC3 SLITRK4 SPANXN2 SPANXN1
TMEM185A MAGEA8 CXorf40B MAMLD1 GPR50 LOC203547 PASD1 MAGEA4 GABRE MAGEA3 PNMA3
ZNF275 VBP1 TMLHE SPRY3 VAMP7 Sum(Control)
-AGACCAGCTTGG 0 0 0 0 0 0 0 0 1 0 0 0 2 0 1 0 4 0 3 1 0 0 0 0 1
2 2 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1 0
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 2 0 0 0 0 0
0 1 0 0 0 0 1 1 1 2 1 0 0 0 0 0 4 0 0 0 0 0 0 0 0 1 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 38 XLMR
-CTCAGAAAAAAA 1 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 4 0 0 0 0 0 0 1 0
0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 1 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 1 0 0 0 2 0 1 0 0 0 0 1
0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 1 27 XLMR
-CCATCCATCCATCCATCC 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 XLMR
-AGAGGGAGAGGG 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0
0 0 2 0 0 0 0 0 1 0 0 0 3 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0
0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 2 0 0 0 0 0 0 0
0 2 1 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 26 XLMR
-ATCTGTTGATGG 0 1 0 0 1 0 0 1 0 1 1 0 2 1 1 1 10 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1
0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
0 1 0 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0
0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 XLMR
-AGGGGTGACAGA 0 1 2 0 0 0 2 0 0 0 0 0 0 0 0 1 6 0 0 0 0 0 0 0 0
0 0 0 0 1 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 1
0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 1 1 0 0
0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 2 0 0 0 0 0 0 0 1 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 28 XLMR
-ATCCCATTTACA 0 0 2 0 0 1 0 0 0 0 1 0 1 0 0 1 6 1 0 0 0 0 0 0 0
0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 2 0 1 0 0 0 0 1 0 0 0 0 1
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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