plotGenes {Sushi} | R Documentation |
plots gene structure or transcript structures
plotGenes(geneinfo = NULL, chrom = NULL, chromstart = NULL, chromend = NULL, col = SushiColors(2)(2)[1], bheight = 0.3, lheight = 0.3, bentline = TRUE, packrow = TRUE, maxrows = 10000, colorby = NULL, colorbyrange = NULL, colorbycol = colorRampPalette(c("blue", "red")), types = "exon", plotgenetype = "box", arrowlength = 0.005, wigglefactor = 0.05, labeltext = TRUE, labeloffset = 0.4, fontsize = 0.7, fonttype = 2, labelat = "middle", ...)
geneinfo |
gene info stored in a bed-like format. If NULL it will look up genes in the region using biomart (with biomart="ensembl" and dataset="hsapiens_gene_ensembl"). See also |
chrom |
chromosome of region to be plotted |
chromstart |
start position |
chromend |
end position |
col |
single value or vector specifying colors of gene structures |
bheight |
the height of the boxes drawn for exons |
lheight |
the height of the bent line is bent is set to TRUE |
bentline |
TRUE/FALSE indicating whether lines between exons should be bent |
packrow |
TRUE / FALSE indicating whether genes should be packed or whether each gene should be plotted on its own row |
maxrows |
The maximum number of rows to plot on the y-axis |
colorby |
vector to scale colors by |
colorbyrange |
the range of values to apply the color scale to. Values outside that range will be set to the limits of the range. |
colorbycol |
palette to apply color scale to (only valid when colorby is not NULL) |
types |
single value or vector specifying types of elements (acceptable values are 'exon','utr') |
plotgenetype |
String specifying whether the genes should resemble a 'box' or a 'arrow' |
arrowlength |
value (between 0 and 1) specifying the length of the tail of each arrow as a fraction of the total plot width (only valid when plotgenetype is set to "arrow") |
wigglefactor |
the fraction of the plot to leave blank on either side of each element to avoid overcrowding. |
labeltext |
TRUE/FALSE indicating whether genes should be labeled |
labeloffset |
value (between 0 and 1) specifying the vertical offset of gene labels |
fontsize |
font size of gene labels |
fonttype |
font type of gene labels |
labelat |
postion along gene to place labels (acceptable values are "middle","start",and "end") |
... |
values to be passed to |
data(Sushi_genes.bed) chrom = "chr15" chromstart = 72998000 chromend = 73020000 chrom_biomart = 15 plotGenes(Sushi_genes.bed,chrom_biomart,chromstart,chromend ,types=Sushi_genes.bed$type, maxrows=1,height=0.5,plotgenetype="arrow",bentline=FALSE,col="blue", labeloffset=1,fontsize=1.2) labelgenome( chrom, chromstart,chromend,side=1,scipen=20,n=3,scale="Mb",line=.18,chromline=.5,scaleline=0.5)