Introduction:

This tool performs a principal components analysis on the inputted peak table data. If the group design file (a Tab-delimited text file) is provided, samples in the same group will be plotted as the same color.

Input files:

1. Peak table file in Tab-delimited txt format, with the first column as compound identifier, the others as samples.

For example:

	HU_011	HU_014	HU_015	HU_017	HU_018	HU_019
(2-methoxyethoxy)propanoic acid isomer	3.019766	3.814339	3.519691	2.562183	3.781922	4.161074
(gamma)Glu-Leu/Ile	3.888479	4.277149	4.195649	4.32376	4.629329	4.412266
1-Methyluric acid	3.869006	3.837704	4.102254	4.53852	4.178829	4.516805
1-Methylxanthine	3.717259	3.776851	4.291665	4.432216	4.11736	4.562052
1,3-Dimethyluric acid	3.535461	3.932581	3.955376	4.228491	4.005545	4.320582
1,7-Dimethyluric acid	3.325199	4.025125	3.972904	4.109927	4.024092	4.326856
2-acetamido-4-methylphenyl acetate	4.204754	5.181858	3.88568	4.237915	1.852994	4.080681
2-Aminoadipic acid	4.080204	4.359246	4.249111	4.231404	4.323679	4.244485

1. (Optional), Group design file in Tab-delimited text file with two column (samplename groupname).

For example:

HU_011	M
HU 014	F
HU_015	M
HU_017	M
HU_018	M
HU_019	M

Output files:

1. 'PCA_Score.txt', PCs (scores) matrix.

2. 'PCA_R2.txt', importance of PCs.

3. 'PCA_Screeplot.pdf', scree plot of variance explained (R2).

4. 'PC12_Score_2D_Label.pdf', PCA scatter plot using PCs score values with the sample name label, PC12 refers to PC1 vs PC2.

5. 'PC12_Score_2D.pdf', PCA scatter plot using PCs score values without the sample name label, PC12 refers to PC1 vs PC2.