Plot PCA

Description

Plot a Principal Component Analysis (PCA) from a data matrix

Input files

Parameters

Apply the log 10

To normalize your data

(?)Add file with metadata on matrix experiment?

To ad metadata to the analysis

Input Metadata file

Must countain a key column named labExpId

Others Metadata files

Choose the fields in the metadata you want to color by

Choose the fields in the metadata you want to shape by

Height of the plot in inches

default 7 inches

Width of the plot in inches

default 7 inches

Output name

Specify the project label for your outputs. By default it will be the name of your input file

Output files

<Input Name>_PCA.pdf

Pdf file containing your PCA plot

Authors Alessandra Breschi (alessandra.breschi@crg.eu); Sarah Djebali (sarah.djebali-quelen@inra.fr); Valentin Marcon (valentin.marcon@inra.fr)

Contact : sigenae-support@listes.inra.fr

Please cite :

• (Depending on the help provided you can cite us in acknowledgements)

Acknowledgements

We wish to thank : Alessandra Breschi, Sarah Djebali (Centre for Genomic Regulation - http://www.crg.eu/), and Valentin Marcon (Migale platform - http://migale.jouy.inra.fr/)

Usage: ./plot_pca.R [options] file

Options:

-i INPUT_MATRIX, --input_matrix=INPUT_MATRIX
	the matrix you want to analyze. Can be stdin
-l, --log10	apply the log [default=FALSE]
-p PSEUDOCOUNT, --pseudocount=PSEUDOCOUNT
	specify a pseudocount for the log [default=1e-04]
-m METADATA, --metadata=METADATA
	A list of tsv files with metadata on matrix experiment. They must be in the format 'file1.tsv,file2.tsv' and contain a key column named 'labExpId'. Can be omitted
--merge_mdata_on=MERGE_MDATA_ON
	[default=labExpId]
-c COLOR_BY, --color_by=COLOR_BY
	choose the fields in the metadata you want to color by
--sort_color=SORT_COLOR
	A field for sorting colors. Can be omitted [default=NULL]
-s SHAPE_BY, --shape_by=SHAPE_BY
	choose the fields in the metadata you want to shape by
--no_legend	Do not show the legend [default=FALSE]
-r, --row_as_variables
	select this if you want rows as variables [default=FALSE]
-C PRINCOMP, --princomp=PRINCOMP
	choose the principal components you want to plot. With 3 PC it gives a 3d plot [default='PC1,PC2']
--print_scores	Output the resuling PCs as a separate file with the extension PCs.tsv [default=FALSE]
--print_loadings
	Output the resulting loadings as a separate file with the extension loadings.tsv [default=FALSE]
--print_lambdas
	Output the resulting lambdas (stdev) as a separate file with the extension lambdas.tsv [default=FALSE]
--biplot	If active, the factor of the color is used as grouping factor. Centroids are computed and the first <top> loadings are plotted wrt to the two specified components [default=FALSE]
--palette=PALETTE
	File with the color palette [default=/users/rg/abreschi/R/palettes/cbbPalette1.15.txt]
--border	Black border to dots [default=FALSE]
--shapes=SHAPES
	File with the shapes [default=NULL]
-L LABELS, --labels=LABELS
	The metadata field with the labels [default=NULL]
-B BASE_SIZE, --base_size=BASE_SIZE
	Base font size [default=16]
-H HEIGHT, --height=HEIGHT
	Height of the plot in inches [default=7]
-W WIDTH, --width=WIDTH
	Width of the plot in inches [default=7]
-o OUTPUT, --output=OUTPUT
	output file name [default=pca.out]
-v, --verbose	verbose output [default=FALSE]
-h, --help	Show this help message and exit