plot_genes {ARTP} | R Documentation |
Plot the observed SNP p-values for each gene
plot_genes(obs.outfile, gene.list, op=NULL)
obs.outfile |
The output file of observed p-values from |
gene.list |
See |
op |
List of options. See |
If the option gene.list$chrm.var
is not specified, then it is assumed that all the SNPs
are on the same chromosome, and the same color will be used in the plot. If gene.list$chrm.var
is specified, then the genes will be grouped by chromosome with the same color for the group.
Options list:
Below are the names for the options list op
.
cex.axis
See par
colors
Colors to use for each gene in the plot
maxLabelLen
Maximum length of x-axis labels
chr.text
See par
x.las
See par
x.padj
See par
A data frame containing the SNP ids, parameter estimates, genes, etc.
# Get the file of observed p-values obs_file <- system.file("sampleData", "obs_pvalues.txt", package="ARTP") # Define the gene-SNP list gs_file <- system.file("sampleData", "gene_SNP_data.txt", package="ARTP") gene.list <- list(file=gs_file, delimiter="\t", header=1, snp.var="SNP", gene.var="Gene") plot_genes(obs_file, gene.list)