snp.plotter Rpad Interface

snp.plotter creates plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple datasets simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. More information is provided on the snp.plotter website.

SNP Image Name:

Image Title:

Dataset Label:

P-value Threshold:

Scale length of connecting lines by this factor:

SNP Color:

Symbol:

LD Map Color Scheme:

LD Metric:

Y-axis scale:

Display Type:

Image Type:

Image Size (in inches):

Distribute SNPs evenly on plot?

Use global p-values?

Display LD heat map color bar?

Display a label showing the range of the X-axis?

Display evenly spaced X-axis tick-labels?

Display lines at p-value thresholds of 0.05, 0.01, 0.001, etc.?

Display legend?

Display SNPs?

Display haplotypes?

Display LD heat map?

SNP Data Input: Copy and paste

Haplotype Data Input: Copy and paste

Pedigree Data Input: Copy and paste 



library(grid)
library(lattice)
library(genetics) 
library(snp.plotter)

IMAGE_FILE <- paste(IMAGE_NAME, ".", IMAGE_TYPE, sep="")

snp.plotter(SNP_FILE = "snp_data.txt", 
		 HAP_FILE = "hap_data.txt", 
		 GENOTYPE_FILE = "genotype.txt", 
		 LAB_Y = LAB_Y, 
		 SYMBOLS = SYMBOLS,
		 EVEN_SPACED = EVEN_SPACED, 
		 PVAL_THRESHOLD = PVAL_THRESHOLD, 
		 USE_GBL_PVAL = USE_GBL_PVAL, 
		 DISP_TYPE = DISP_TYPE, 
		 DISP_LDMAP = DISP_LDMAP, 
		 DISP_HAP = DISP_HAP, 
		 DISP_SNP = DISP_SNP, 
		 DISP_MARKER_LINES = DISP_MARKER_LINES, 
		 LD_COLOR_SCHEME = LD_COLOR_SCHEME, 
		 COLOR_LIST = COLOR_LIST, 
		 LD_TYPE = LD_TYPE, 
		 DISP_COLOR_BAR = DISP_COLOR_BAR,
		 DISP_PHYS_DIST = DISP_PHYS_DIST,
		 IMAGE_TITLE = IMAGE_TITLE, 
		 DISP_LEGEND = DISP_LEGEND, 
		 DATASET_LABELS = DATASET_LABELS, 
		 IMAGE_TYPE = IMAGE_TYPE, 
		 IMAGE_SIZE = IMAGE_SIZE,
		 DISP_MULT_LAB_X = DISP_MULT_LAB_X, 
		 IMAGE_NAME = IMAGE_NAME,
		 CONNECTING_LINES_FACTOR = CONNECTING_LINES_FACTOR)

cat("Done.\nImage Location: ", paste(getwd(), .Platform$file.sep, IMAGE_FILE, sep=""), "\n")