maaslin: maaslin-4450aa4ecc84/src/lib/scriptBiplotTSV.R annotate

annotate maaslin-4450aa4ecc84/src/lib/scriptBiplotTSV.R @ 1:a87d5a5f2776

Uploaded the version running on the prod server

author	george-weingart
date	Sun, 08 Feb 2015 23:08:38 -0500
parents
children

rev	line source
1 a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	1 #!/usr/bin/env Rscript
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	3 library(vegan)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	4 library(optparse)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	6 funcGetCentroidForMetadatum <- function(
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	7 ### Given a binary metadatum, calculate the centroid of the samples associated with the metadata value of 1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	8 # 1. Get all samples that have the metadata value of 1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	9 # 2. Get the x and y coordinates of the selected samples
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	10 # 3. Get the median value for the x and ys
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	11 # 4. Return those coordinates as the centroid's X and Y value
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	12 vfMetadata,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	13 ### Logical or integer (0,1) vector, TRUE or 1 values indicate correspoinding samples in the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	14 ### mSamplePoints which will be used to define the centroid
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	15 mSamplePoints
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	16 ### Coordinates (columns;n=2) of samples (rows) corresponding to the vfMetadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	17 ){
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	18 # Check the lengths which should be equal
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	19 if(length(vfMetadata)!=nrow(mSamplePoints))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	20 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	21 print(paste("funcGetCentroidForMetadata::Error: Should have received metadata and samples of the same length, received metadata length ",length(vfMetadata)," and sample ",nrow(mSamplePoints)," length.",sep=""))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	22 return( FALSE )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	23 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	24
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	25 # Get all the samples that have the metadata value of 1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	26 viMetadataSamples = which(as.integer(vfMetadata)==1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	27
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	28 # Get the x and y coordinates for the selected samples
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	29 mSelectedPoints = mSamplePoints[viMetadataSamples,]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	30
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	31 # Get the median value for the x and the ys
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	32 if(!is.null(nrow(mSelectedPoints)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	33 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	34 return( list(x=median(mSelectedPoints[,1],na.rm = TRUE),y=median(mSelectedPoints[,2],na.rm = TRUE)) )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	35 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	36 return( list(x=mSelectedPoints[1],y=mSelectedPoints[2]) )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	37 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	38 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	39
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	40 funcGetMaximumForMetadatum <- function(
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	41 ### Given a continuous metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	42 ### 1. Use the x and ys from mSamplePoints for coordinates and the metadata value as a height (z)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	43 ### 2. Use lowess to smooth the landscape
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	44 ### 3. Take the maximum of the landscape
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	45 ### 4. Return the coordiantes for the maximum as the centroid
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	46 vdMetadata,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	47 ### Continuous (numeric or integer) metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	48 mSamplePoints
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	49 ### Coordinates (columns;n=2) of samples (rows) corresponding to the vfMetadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	50 ){
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	51 # Work with data frame
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	52 if(class(mSamplePoints)=="matrix")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	53 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	54 mSamplePoints = data.frame(mSamplePoints)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	55 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	56 # Check the lengths of the dataframes and the metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	57 if(length(vdMetadata)!=nrow(mSamplePoints))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	58 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	59 print(paste("funcGetMaximumForMetadatum::Error: Should have received metadata and samples of the same length, received metadata length ",length(vdMetadata)," and sample ",nrow(mSamplePoints)," length.",sep=""))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	60 return( FALSE )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	61 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	62
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	63 # Add the metadata value to the points
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	64 mSamplePoints[3] = vdMetadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	65 names(mSamplePoints) = c("x","y","z")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	66
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	67 # Create lowess to smooth the surface
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	68 # And calculate the fitted heights
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	69 # x = sample coordinate 1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	70 # y = sample coordinate 2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	71 # z = metadata value
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	72 loessSamples = loess(z~x*y, data=mSamplePoints, degree = 1, normalize = FALSE, na.action=na.omit)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	73
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	74 # Naively get the max
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	75 vdCoordinates = loessSamples$x[which(loessSamples$y==max(loessSamples$y)),]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	76 return(list(lsmod = loessSamples, x=vdCoordinates[1],y=vdCoordinates[2]))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	77 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	78
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	79 funcMakeShapes <- function(
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	80 ### Takes care of defining shapes for the plot
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	81 dfInput,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	82 ### Data frame of metadata measurements
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	83 sShapeBy,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	84 ### The metadata to shape by
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	85 sShapes,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	86 ### List of custom metadata (per level if factor).
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	87 ### Should correspond to the number of levels in shapeBy; the format is level:shape,level:shape for example HighLuminosity:14,LowLuminosity:2,HighPH:10,LowPH:18
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	88 cDefaultShape
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	89 ### Shape to default to if custom shapes are not used
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	90 ){
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	91 lShapes = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	92 vsShapeValues = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	93 vsShapeShapes = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	94 vsShapes = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	95 sMetadataId = sShapeBy
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	96
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	97 # Set default shape, color, and color ranges
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	98 if(!is.null(cDefaultShape))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	99 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	100 # Default shape should be an int for the int pch options
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	101 if(!is.na(as.integer(cDefaultShape)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	102 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	103 cDefaultShape = as.integer(cDefaultShape)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	104 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	105 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	106 cDefaultShape = 16
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	107 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	108
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	109 # Make shapes
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	110 vsShapes = rep(cDefaultShape,nrow(dfInput))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	111
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	112 if(!is.null(sMetadataId))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	113 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	114 if(is.null(sShapes))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	115 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	116 vsShapeValues = unique(dfInput[[sMetadataId]])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	117 vsShapeShapes = 1:length(vsShapeValues)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	118 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	119 # Put the markers in the order of the values)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	120 vsShapeBy = unlist(strsplit(sShapes,","))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	121 for(sShapeBy in vsShapeBy)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	122 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	123 vsShapeByPieces = unlist(strsplit(sShapeBy,":"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	124 lShapes[vsShapeByPieces[1]] = as.integer(vsShapeByPieces[2])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	125 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	126 vsShapeValues = names(lShapes)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	127 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	128
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	129 # Shapes in the correct order
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	130 if(!is.null(sShapes))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	131 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	132 vsShapeShapes = unlist(lapply(vsShapeValues,function(x) lShapes[[x]]))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	133 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	134 vsShapeValues = paste(vsShapeValues)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	135
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	136 # Make the list of shapes
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	137 for(iShape in 1:length(vsShapeValues))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	138 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	139 vsShapes[which(paste(dfInput[[sMetadataId]])==vsShapeValues[iShape])]=vsShapeShapes[iShape]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	140 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	141
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	142 # If they are all numeric characters, make numeric
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	143 viIntNas = which(is.na(as.integer(vsShapes)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	144 viNas = which(is.na(vsShapes))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	145 if(length(setdiff(viIntNas,viNas))==0)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	146 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	147 vsShapes = as.integer(vsShapes)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	148 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	149 print("funcMakeShapes::Error: Please supply numbers 1-25 for shape in the -y,--shapeBy option")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	150 vsShapeValues = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	151 vsShapeShapes = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	152 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	153 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	154 return(list(PlotShapes=vsShapes,Values=vsShapeValues,Shapes=vsShapeShapes,ID=sMetadataId,DefaultShape=cDefaultShape))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	155 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	156
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	157 ### Global defaults
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	158 c_sDefaultColorBy = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	159 c_sDefaultColorRange = "orange,cyan"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	160 c_sDefaultTextColor = "black"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	161 c_sDefaultArrowColor = "cyan"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	162 c_sDefaultArrowTextColor = "Blue"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	163 c_sDefaultNAColor = "grey"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	164 c_sDefaultShapeBy = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	165 c_sDefaultShapes = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	166 c_sDefaultMarker = "16"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	167 c_sDefaultRotateByMetadata = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	168 c_sDefaultResizeArrow = 1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	169 c_sDefaultTitle = "Custom Biplot of Bugs and Samples - Metadata Plotted with Centroids"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	170 c_sDefaultOutputFile = NULL
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	171
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	172 ### Create command line argument parser
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	173 pArgs <- OptionParser( usage = "%prog last_metadata input.tsv" )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	174
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	175 # Selecting features to plot
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	176 pArgs <- add_option( pArgs, c("-b", "--bugs"), type="character", action="store", default=NULL, dest="sBugs", metavar="BugsToPlot", help="Comma delimited list of data to plot as text. Bug\|1,Bug\|2")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	177 pArgs <- add_option( pArgs, c("-m", "--metadata"), type="character", action="store", default=NULL, dest="sMetadata", metavar="MetadataToPlot", help="Comma delimited list of metadata to plot as arrows. metadata1,metadata2,metadata3")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	178
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	179 # Colors
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	180 pArgs <- add_option( pArgs, c("-c", "--colorBy"), type="character", action="store", default=c_sDefaultColorBy, dest="sColorBy", metavar="MetadataToColorBy", help="The id of the metadatum to use to make the marker colors. Expected to be a continuous metadata.")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	181 pArgs <- add_option( pArgs, c("-r", "--colorRange"), type="character", action="store", default=c_sDefaultColorRange, dest="sColorRange", metavar="ColorRange", help=paste("Colors used to color the samples; a gradient will be formed between the color.Default=", c_sDefaultColorRange))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	182 pArgs <- add_option( pArgs, c("-t", "--textColor"), type="character", action="store", default=c_sDefaultTextColor, dest="sTextColor", metavar="TextColor", help=paste("The color bug features will be plotted with as text. Default =", c_sDefaultTextColor))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	183 pArgs <- add_option( pArgs, c("-a", "--arrowColor"), type="character", action="store", default=c_sDefaultArrowColor, dest="sArrowColor", metavar="ArrowColor", help=paste("The color metadata features will be plotted with as an arrow and text. Default", c_sDefaultArrowColor))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	184 pArgs <- add_option( pArgs, c("-w", "--arrowTextColor"), type="character", action="store", default=c_sDefaultArrowTextColor, dest="sArrowTextColor", metavar="ArrowTextColor", help=paste("The color for the metadata text ploted by the head of the metadata arrow. Default", c_sDefaultArrowTextColor))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	185 pArgs <- add_option(pArgs, c("-n","--plotNAColor"), type="character", action="store", default=c_sDefaultNAColor, dest="sPlotNAColor", metavar="PlotNAColor", help=paste("Plot NA values as this color. Example -n", c_sDefaultNAColor))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	186
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	187 # Shapes
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	188 pArgs <- add_option( pArgs, c("-y", "--shapeby"), type="character", action="store", default=c_sDefaultShapeBy, dest="sShapeBy", metavar="MetadataToShapeBy", help="The metadata to use to make marker shapes. Expected to be a discrete metadatum. An example would be -y Environment")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	189 pArgs <- add_option( pArgs, c("-s", "--shapes"), type="character", action="store", default=c_sDefaultShapes, dest="sShapes", metavar="ShapesForPlotting", help="This is to be used to specify the shapes to use for plotting. Can use numbers recognized by R as shapes (see pch). Should correspond to the number of levels in shapeBy; the format is level:shape,level:shape for example HighLuminosity:14,LowLuminosity:2,HighPH:10,LowPH:18 . Need to specify -y/--shapeBy for this option to work.")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	190 pArgs <- add_option( pArgs, c("-d", "--defaultMarker"), type="character", action="store", default=c_sDefaultMarker, dest="sDefaultMarker", metavar="DefaultColorMarker", help="Default shape for markers which are not otherwise indicated in --shapes, can be used for unspecified values or NA. Must not be a shape in --shapes.")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	191
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	192 # Plot manipulations
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	193 pArgs <- add_option( pArgs, c("-e","--rotateByMetadata"), type="character", action="store", default=c_sDefaultRotateByMetadata, dest="sRotateByMetadata", metavar="RotateByMetadata", help="Rotate the ordination by a metadata. Give both the metadata and value to weight it by. The larger the weight, the more the ordination is influenced by the metadata. If the metadata is continuous, use the metadata id; if the metadata is discrete, the ordination will be by one of the levels so use the metadata ID and level seperated by a '_'. Discrete example -e Environment_HighLumninosity,100 ; Continuous example -e Environment,100 .")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	194 pArgs <- add_option( pArgs, c("-z","--resizeArrow"), type="numeric", action="store", default=c_sDefaultResizeArrow, dest="dResizeArrow", metavar="ArrowScaleFactor", help="A constant to multiple the length of the arrow to expand or shorten all arrows together. This will not change the angle of the arrow nor the relative length of arrows to each other.")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	195
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	196 # Misc
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	197 pArgs <- add_option( pArgs, c("-i", "--title"), type="character", action="store", default=c_sDefaultTitle, dest="sTitle", metavar="Title", help="This is the title text to add to the plot.")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	198 pArgs <- add_option( pArgs, c("-o", "--outputfile"), type="character", action="store", default=c_sDefaultOutputFile, dest="sOutputFileName", metavar="OutputFile", help="This is the name for the output pdf file. If an output file is not given, an output file name is made based on the input file name.")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	199
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	200 funcDoBiplot <- function(
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	201 ### Perform biplot. Samples are markers, bugs are text, and metadata are text with arrows. Markers and bugs are dtermined usiing NMDS and Bray-Curtis dissimilarity. Metadata are placed on the ordination in one of two ways: 1. Factor data - for each level take the ordination points for the samples that have that level and plot the metadata text at the average orindation point. 2. For continuous data - make a landscape (x and y form ordination of the points) and z (height) as the metadata value. Use a lowess line to get the fitted values for z and take the max of the landscape. Plot the metadata text at that smoothed max.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	202 sBugs,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	203 ### Comma delimited list of data to plot as text. Bug\|1,Bug\|2
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	204 sMetadata,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	205 ### Comma delimited list of metadata to plot as arrows. metadata1,metadata2,metadata3.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	206 sColorBy = c_sDefaultColorBy,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	207 ### The id of the metadatum to use to make the marker colors. Expected to be a continuous metadata.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	208 sColorRange = c_sDefaultColorRange,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	209 ### Colors used to color the samples; a gradient will be formed between the color. Example orange,cyan
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	210 sTextColor = c_sDefaultTextColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	211 ### The color bug features will be plotted with as text. Example black
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	212 sArrowColor = c_sDefaultArrowColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	213 ### The color metadata features will be plotted with as an arrow and text. Example cyan
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	214 sArrowTextColor = c_sDefaultArrowTextColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	215 ### The color for the metadata text ploted by the head of the metadata arrow. Example Blue
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	216 sPlotNAColor = c_sDefaultNAColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	217 ### Plot NA values as this color. Example grey
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	218 sShapeBy = c_sDefaultShapeBy,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	219 ### The metadata to use to make marker shapes. Expected to be a discrete metadatum.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	220 sShapes = c_sDefaultShapes,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	221 ### This is to be used to specify the shapes to use for plotting. Can use numbers recognized by R as shapes (see pch). Should correspond to the number of levels in shapeBy; the format is level:shape,level:shape for example HighLuminosity:14,LowLuminosity:2,HighPH:10,LowPH:18 . Works with sShapesBy.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	222 sDefaultMarker = c_sDefaultMarker,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	223 ### The default marker shape to use if shapes are not otherwise indicated.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	224 sRotateByMetadata = c_sDefaultRotateByMetadata,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	225 ### Metadata and value to rotate by. example Environment_HighLumninosity,100
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	226 dResizeArrow = c_sDefaultResizeArrow,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	227 ### Scale factor to resize tthe metadata arrows
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	228 sTitle = c_sDefaultTitle,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	229 ### The title for the figure.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	230 sInputFileName,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	231 ### File to input (tsv file: tab separated, row = sample file)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	232 sLastMetadata,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	233 ### Last metadata that seperates data and metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	234 sOutputFileName = c_sDefaultOutputFile
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	235 ### The file name to save the figure.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	236 ){
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	237 print("IN Biplot")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	238 # Define the colors
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	239 vsColorRange = c("blue","orange")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	240 cDefaultColor = "black"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	241 if(!is.null(sColorRange))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	242 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	243 vsColorRange = unlist(strsplit(sColorRange,","))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	244 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	245
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	246 # List of bugs to plot
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	247 # If there is a list it needs to be more than one.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	248 vsBugsToPlot = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	249 if(!is.null(sBugs))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	250 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	251 vsBugsToPlot = unlist(strsplit(sBugs,","))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	252 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	253
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	254 print("vsBugsToPlot")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	255 print(vsBugsToPlot)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	256 # Metadata to plot
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	257 vsMetadata = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	258 if(!is.null(sMetadata))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	259 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	260 vsMetadata = unlist(strsplit(sMetadata,","))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	261 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	262
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	263 print("vsMetadata")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	264 print(vsMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	265 ### Load table
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	266 if(class(sInputFileName)=="character")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	267 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	268 dfInput = read.table(sInputFileName, sep = "\t", header=TRUE)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	269 names(dfInput) = unlist(lapply(names(dfInput),function(x) gsub(".","\|",x,fixed=TRUE)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	270 row.names(dfInput) = dfInput[,1]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	271 dfInput = dfInput[-1]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	272 } else {dfInput = sInputFileName}
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	273
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	274 ### Get positions of all metadata or all data
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	275 iLastMetadata = which(names(dfInput)==sLastMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	276 viMetadata = 1:iLastMetadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	277 viData = (iLastMetadata+1):ncol(dfInput)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	278
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	279 ### Dummy the metadata if discontinuous
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	280 ### Leave the continous metadata alone but include
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	281 listMetadata = list()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	282 vsRowNames = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	283 viContinuousMetadata = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	284 for(i in viMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	285 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	286 print( names( dfInput )[i] )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	287 vCurMetadata = unlist(dfInput[i])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	288 if( ( is.numeric(vCurMetadata)\|\|is.integer(vCurMetadata) ) && ( length( unique( vCurMetadata ) ) >= c_iNonFactorLevelThreshold ) )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	289 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	290 vCurMetadata[which(is.na(vCurMetadata))] = mean(vCurMetadata,na.rm=TRUE)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	291 listMetadata[[length(listMetadata)+1]] = vCurMetadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	292 vsRowNames = c(vsRowNames,names(dfInput)[i])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	293 viContinuousMetadata = c(viContinuousMetadata,length(listMetadata))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	294 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	295 vCurMetadata = as.factor(vCurMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	296 vsLevels = levels(vCurMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	297 for(sLevel in vsLevels)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	298 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	299 vNewMetadata = rep(0,length(vCurMetadata))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	300 vNewMetadata[which(vCurMetadata == sLevel)] = 1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	301 listMetadata[[length(listMetadata)+1]] = vNewMetadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	302 vsRowNames = c(vsRowNames,paste(names(dfInput)[i],sLevel,sep="_"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	303 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	304 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	305 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	306
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	307 # Convert to data frame
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	308 dfDummyMetadata = as.data.frame(sapply(listMetadata,rbind))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	309 names(dfDummyMetadata) = vsRowNames
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	310 iNumberMetadata = ncol(dfDummyMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	311
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	312 # Data to use in ordination in NMDS
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	313 # All cleaned bug data
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	314 dfData = dfInput[viData]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	315
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	316 # If rotating the ordination by a metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	317 # 1. Add in the metadata as a bug
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	318 # 2. Multiply the bug by the weight
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	319 # 3. Push this through the NMDS
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	320 if(!is.null(sRotateByMetadata))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	321 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	322 vsRotateMetadata = unlist(strsplit(sRotateByMetadata,","))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	323 sMetadata = vsRotateMetadata[1]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	324 dWeight = as.numeric(vsRotateMetadata[2])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	325 sOrdinationMetadata = dfDummyMetadata[sMetadata]*dWeight
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	326 dfData[sMetadata] = sOrdinationMetadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	327 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	328
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	329 # Run NMDS on bug data (Default B-C)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	330 # Will have species and points because working off of raw data
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	331 mNMDSData = metaMDS(dfData,k=2)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	332
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	333 ## Make shapes
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	334 # Defines the shapes and the metadata they are based on
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	335 # Metadata to use as shapes
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	336 lShapeInfo = funcMakeShapes(dfInput=dfInput, sShapeBy=sShapeBy, sShapes=sShapes, cDefaultShape=sDefaultMarker)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	337
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	338 sMetadataShape = lShapeInfo[["ID"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	339 vsShapeValues = lShapeInfo[["Values"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	340 vsShapeShapes = lShapeInfo[["Shapes"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	341 vsShapes = lShapeInfo[["PlotShapes"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	342 cDefaultShape = lShapeInfo[["DefaultShape"]]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	343
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	344 # Colors
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	345 vsColors = rep(cDefaultColor,nrow(dfInput))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	346 vsColorValues = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	347 vsColorRBG = c()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	348 if(!is.null(sColorBy))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	349 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	350 vsColorValues = paste(sort(unique(unlist(dfInput[[sColorBy]])),na.last=TRUE))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	351 iLengthColorValues = length(vsColorValues)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	352
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	353 vsColorRBG = lapply(1:iLengthColorValues/iLengthColorValues,colorRamp(vsColorRange))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	354 vsColorRBG = unlist(lapply(vsColorRBG, function(x) rgb(x[1]/255,x[2]/255,x[3]/255)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	355
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	356 for(iColor in 1:length(vsColorRBG))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	357 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	358 vsColors[which(paste(dfInput[[sColorBy]])==vsColorValues[iColor])]=vsColorRBG[iColor]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	359 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	360
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	361 #If NAs are seperately given color, then color here
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	362 if(!is.null(sPlotNAColor))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	363 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	364 vsColors[which(is.na(dfInput[[sColorBy]]))] = sPlotNAColor
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	365 vsColorRBG[which(vsColorValues=="NA")] = sPlotNAColor
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	366 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	367 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	368
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	369 print("names(dfDummyMetadata)")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	370 print(names(dfDummyMetadata))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	371
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	372 # Reduce the bugs down to the ones in the list to be plotted
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	373 viBugsToPlot = which(row.names(mNMDSData$species) %in% vsBugsToPlot)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	374 viMetadataDummy = which(names(dfDummyMetadata) %in% vsMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	375
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	376 print("viBugsToPlot")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	377 print(viBugsToPlot)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	378 print("viMetadataDummy")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	379 print(names(dfDummyMetadata)[viMetadataDummy])
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	380
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	381 # Build the matrix of metadata coordinates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	382 mMetadataCoordinates = matrix(rep(NA, iNumberMetadata*2),nrow=iNumberMetadata)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	383 for( i in 1:iNumberMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	384 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	385 lxReturn = NA
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	386 if( i %in% viContinuousMetadata )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	387 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	388 lxReturn = funcGetMaximumForMetadatum(dfDummyMetadata[[i]],mNMDSData$points)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	389 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	390 lxReturn = funcGetCentroidForMetadatum(dfDummyMetadata[[i]],mNMDSData$points)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	391 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	392 mMetadataCoordinates[i,] = c(lxReturn$x,lxReturn$y)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	393 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	394 row.names(mMetadataCoordinates) = vsRowNames
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	395
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	396 # Plot the biplot with the centroid constructed metadata coordinates
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	397 if(length(viMetadataDummy)==0)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	398 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	399 viMetadataDummy = 1:nrow(mMetadataCoordinates)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	400 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	401
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	402 # Plot samples
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	403 # Make output name
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	404 if(is.null(sOutputFileName))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	405 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	406 viPeriods = which(sInputFileName==".")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	407 if(length(viPeriods)>0)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	408 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	409 sOutputFileName = paste(OutputFileName[1:viPeriods[length(viPeriods)]],"pdf",sep=".")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	410 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	411 sOutputFileName = paste(sInputFileName,"pdf",sep=".")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	412 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	413 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	414
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	415 pdf(sOutputFileName, useDingbats=FALSE)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	416 plot(mNMDSData$points, xlab=paste("NMDS1","Stress=",mNMDSData$stress), ylab="NMDS2", pch=vsShapes, col=vsColors)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	417 title(sTitle,line=3)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	418
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	419 # Plot Bugs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	420 mPlotBugs = mNMDSData$species[viBugsToPlot,]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	421 if(length(viBugsToPlot)==1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	422 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	423 text(x=mPlotBugs[1],y=mPlotBugs[2],labels=row.names(mNMDSData$species)[viBugsToPlot],col=sTextColor)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	424 } else if(length(viBugsToPlot)>1){
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	425 text(x=mPlotBugs[,1],y=mPlotBugs[,2],labels=row.names(mNMDSData$species)[viBugsToPlot],col=sTextColor)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	426 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	427
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	428 # Add alternative axes
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	429 axis(3, col=sArrowColor)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	430 axis(4, col=sArrowColor)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	431 box(col = "black")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	432
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	433 # Plot Metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	434 if(length(viMetadataDummy)>0)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	435 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	436 for(i in viMetadataDummy)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	437 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	438 curCoordinates = mMetadataCoordinates[i,]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	439 curCoordinates = curCoordinates * dResizeArrow
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	440 # Plot Arrow
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	441 arrows(0,0, curCoordinates[1] * 0.8, curCoordinates[2] * 0.8, col=sArrowColor, length=0.1 )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	442 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	443 # Plot text
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	444 if(length(viMetadataDummy)==1)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	445 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	446 text(x=mMetadataCoordinates[viMetadataDummy,][1]dResizeArrow0.8, y=mMetadataCoordinates[viMetadataDummy,][2]dResizeArrow0.8, labels=row.names(mMetadataCoordinates)[viMetadataDummy],col=sArrowTextColor)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	447 } else {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	448 text(x=mMetadataCoordinates[viMetadataDummy,1]dResizeArrow0.8, y=mMetadataCoordinates[viMetadataDummy,2]dResizeArrow0.8, labels=row.names(mMetadataCoordinates)[viMetadataDummy],col=sArrowTextColor)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	449 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	450 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	451
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	452 # Create Legend
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	453 # The text default is the colorMetadata_level (one per level) plus the ShapeMetadata_level (one per level)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	454 # The color default is already determined colors plus grey for shapes.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	455 sLegendText = c(paste(vsColorValues,sColorBy,sep="_"),paste(sMetadataShape,vsShapeValues,sep="_"))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	456 sLegendColors = c(vsColorRBG,rep(cDefaultColor,length(vsShapeValues)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	457
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	458 # If the color values are numeric
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	459 # Too many values may be given in the legend (given they may be a continuous range of values)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	460 # To reduce this they are summarized instead, given the colors and values for the extreme ends.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	461 if( !sum( is.na( as.numeric( vsColorValues[ which( !is.na( vsColorValues ) ) ] ) ) ) )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	462 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	463 vdNumericColors = as.numeric( vsColorValues )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	464 vdNumericColors = vdNumericColors[ which( !is.na( vdNumericColors ) ) ]
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	465 vdSortedNumericColors = sort( vdNumericColors )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	466 sLegendText = c( paste( sColorBy, vdSortedNumericColors[ 1 ], sep="_" ),
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	467 paste( sColorBy, vdSortedNumericColors[ length(vdSortedNumericColors) ], sep="_" ),
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	468 paste( sMetadataShape, vsShapeValues, sep="_" ) )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	469 sLegendColors = c(vsColorRBG[ which( vdNumericColors == vdSortedNumericColors[ 1 ] )[ 1 ] ],
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	470 vsColorRBG[ which( vdNumericColors == vdSortedNumericColors[ length( vdSortedNumericColors ) ] )[ 1 ] ],
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	471 rep(cDefaultColor,length(vsShapeValues)))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	472 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	473 sLegendShapes = c( rep( cDefaultShape, length( sLegendText ) - length( vsShapeShapes ) ), vsShapeShapes )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	474
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	475 # If any legend text was constructed then make the legend.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	476 if( length( sLegendText ) >0 )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	477 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	478 legend( "topright", legend = sLegendText, pch = sLegendShapes, col = sLegendColors )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	479 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	480
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	481 # Original biplot call if you want to check the custom plotting of the script
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	482 # There will be one difference where the biplot call scales an axis, this one does not. In relation to the axes, the points, text and arrows should still match.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	483 # Axes to the top and right are for the arrow, others are for markers and bug names.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	484 #biplot(mNMDSData$points,mMetadataCoordinates[viMetadataDummy,],xlabs=vsShapes,xlab=paste("MDS1","Stress=",mNMDSData$stress),main="Biplot function Bugs and Sampes - Metadata Plotted with Centroids")
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	485 dev.off()
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	486 }
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	487
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	488 # This is the equivalent of __name__ == "__main__" in Python.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	489 # That is, if it's true we're being called as a command line script;
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	490 # if it's false, we're being sourced or otherwise included, such as for
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	491 # library or inlinedocs.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	492 if( identical( environment( ), globalenv( ) ) &&
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	493 !length( grep( "^source\\(", sys.calls( ) ) ) )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	494 {
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	495 lsArgs <- parse_args( pArgs, positional_arguments=TRUE )
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	496
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	497 funcDoBiplot(
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	498 sBugs = lsArgs$options$sBugs,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	499 sMetadata = lsArgs$options$sMetadata,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	500 sColorBy = lsArgs$options$sColorBy,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	501 sColorRange = lsArgs$options$sColorRange,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	502 sTextColor = lsArgs$options$sTextColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	503 sArrowColor = lsArgs$options$sArrowColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	504 sArrowTextColor = lsArgs$options$sArrowTextColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	505 sPlotNAColor = lsArgs$options$sPlotNAColor,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	506 sShapeBy = lsArgs$options$sShapeBy,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	507 sShapes = lsArgs$options$sShapes,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	508 sDefaultMarker = lsArgs$options$sDefaultMarker,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	509 sRotateByMetadata = lsArgs$options$sRotateByMetadata,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	510 dResizeArrow = lsArgs$options$dResizeArrow,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	511 sTitle = lsArgs$options$sTitle,
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	512 sInputFileName = lsArgs$args[2],
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	513 sLastMetadata = lsArgs$args[1],
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	514 sOutputFileName = lsArgs$options$sOutputFileName)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	515 }

Mercurial > repos > george-weingart > maaslin

annotate maaslin-4450aa4ecc84/src/lib/scriptBiplotTSV.R @ 1:a87d5a5f2776