Plot a Principal Component Analysis (PCA) from a data matrix
Parameter : num + label | Format |
---|---|
1 : Input matrix | csv,tabular |
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
Usage: ./plot_pca.R [options] file
-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 | |
| |
--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 |
|
--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 |