R PCA using FactoMiner package /usr/local/bioinfo/src/R/current/ pca_FactoMiner_galaxy_wrapper.R datafile $datafile factor $factor npc $npc title $title tc $tc pch $pch pcv $pcv scaleoption $scaleoption plotev $plotev plotcontrib $plotcontrib plotindiv $plotindiv colorfactor $colorfactor plotvar $plotvar contribh $contribh contribv $contribv ## Outputs logOut $logOut outgraphpdf $outgraphpdf None Unit variance Pareto Yes No Yes No Yes No Yes No Yes No .. class:: infomark **Authors** J.F Martin (jean-francois.martin@toulouse.inra.fr) et M. Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) === PCA === ----------- Description ----------- Principal Component Analysis (PCA) as done in the FactoMineR package ----------- Input files ----------- +---------------------------+------------+ | Parameter : num + label | Format | +===========================+============+ | 1 : data matrix name | tabular | +---------------------------+------------+ **Data matrix name** | ... ---------- Parameters ---------- Data matrix name | see "Input files" section above | Factor | Name of the column containing the biological factor (qualitative variable) to color observations according to levels of this | Number of principal component | How many principal components include in the PCA model? | Title | Title printed on all plots; if none, leave 'PCA'" value="PCA" | Numeric character expansion factor | A value greater than 1 increases and a value lower than 1 decreases character size | Horizontal Principal Component | Principal component displayed on the abscissa | Vertical Principal Component | Principal component displayed on the ordinate | Scaling method | Standardisation to apply to the variables | None, Unit variance (default value) or Pareto scaling | Eigenvalue plot | Eigenvalue and percentage of explained variance plots. Default value is "Yes" | Contribution plot | Contribution plot. Default value is "Yes" | Score plot | Score plot" plot. Default value is "Yes" | Factor color | Colouring of observations. Default value is "Yes" | Loading plot | Loading plot. Default value is "Yes" | Contribution threshold (abscissa) | Contribution threshold for loading plot: principal component displayed in the abscissa axis | Contribution threshold (ordinate) | Contribution threshold for loading plot: principal component displayed in the ordinate axis | ------------ Output files ------------ outgraphpdf.pdf | pdf output | ... | ---------------------------------------------------