RCricos绘制简单圈图

程序1：library(RCircos)#导入内建人类染色体数据data(UCSC.HG38.Human.CytoBandIdeogram)cyto.info <- UCSC.HG38.Human.CytoBandIdeogramRCircos.Set.Core.Components(cyto.info, chr.exclude=NULL,tracks.inside=10, tracks.outside=0 )#chr.exclude <- NULL;           设置不显示的染色体，如 c(1,3)          #cyto.info <- UCSC.HG19.Human.CytoBandIdeogram; 设置染色体数据#tracks.inside <- 10;    设置内部track 个数#tracks.outside <- 0;    设置外部track 个数                                                     #设置外部track 个数RCircos.Set.Plot.Area()RCircos.Chromosome.Ideogram.Plot() #绘制染色体表意文字，染色体的默认方法亮点和染色体名称。

程序2：#导入内建人类染色体数据data(UCSC.HG19.Human.CytoBandIdeogram);head(UCSC.HG19.Human.CytoBandIdeogram); chr.exclude <- NULL;                            #设置不显示的染色体，如 c(1,3)           cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;  #设置染色体数据 tracks.inside <- 10;                                                         #设置内部track 个数 tracks.outside <- 0;                                                         #设置外部track 个数  #导入上面四个基本参数 RCircos.Set.Core.Components(cyto.info, chr.exclude, tracks.inside, tracks.outside);#列出 所有绘图参数RCircos.List.Parameters() #Following are an example to change RCircos plot parameters:#===========================================================params <- RCircos.Get.Plot.Parameters();  #获得参数列表params$radius.len <- 2.0;                                    #更改其中的参数            params$base.per.unit <- 5000;                            #更改其中的参数            RCircos.Reset.Plot.Parameters(params)     #参数重置   #定义要生成的图像文件，pdf，png，tiff 等 ，注意：最后要用dev.off()关闭 out.file <- "D:/RCircosDemoHumanGenome.tiff"; pdf(file=out.file, height=8, width=8, compress=TRUE); RCircos.Set.Plot.Area();#Plot Chromosome IdeogramRCircos.Chromosome.Ideogram.Plot();

#Gene Labels and connectors on RCircos Plot#RCircos.Gene.Connector.Plot   绘制染色体表意文字和基因名称之间的连接#RCircos.Gene.Name.Plot 在数据轨道上绘制基因名称data(RCircos.Gene.Label.Data);name.col <- 4;side <- "in";track.num <- 1;RCircos.Gene.Connector.Plot(RCircos.Gene.Label.Data, track.num, side);track.num <- 2;RCircos.Gene.Name.Plot(RCircos.Gene.Label.Data, name.col,track.num, side);#Heatmap, Histogram, Line, Scatter, and Tile Plot#Heatmap--------------#RCircos.Heatmap.Plot绘制一个数据轨道的热图data(RCircos.Heatmap.Data); data.col <- 6; track.num <- 5; side <- "in"; RCircos.Heatmap.Plot(RCircos.Heatmap.Data, data.col, track.num, side); #Scatter-------------- #RCircos.Scatter.Plot  一个数据轨迹的扫描图 data(RCircos.Scatter.Data); data.col <- 5; track.num <- 6; side <- "in"; by.fold <- 1; RCircos.Scatter.Plot(RCircos.Scatter.Data, data.col,track.num, side, by.fold); #Line----------------- #RCircos.Line.Plot绘制线为一个数据轨道 data(RCircos.Line.Data); data.col <- 5; track.num <- 7; side <- "in"; RCircos.Line.Plot(RCircos.Line.Data, data.col, track.num, side); #Histogram------------ #RCircos.Histogram.Plot  绘制一个数据轨迹的直方图 data(RCircos.Histogram.Data); data.col <- 4; track.num <- 8; side <- "in"; RCircos.Histogram.Plot(RCircos.Histogram.Data, data.col, track.num, side); # Tile----------------- data(RCircos.Tile.Data); track.num <- 9; side <- "in"; RCircos.Tile.Plot(RCircos.Tile.Data, track.num, side);#Links-----------------#RCircos.Link.Plot绘制两个或多个基因组位置之间的链接线data(RCircos.Link.Data);track.num <- 11;RCircos.Link.Plot(RCircos.Link.Data, track.num, TRUE);data(RCircos.Ribbon.Data);RCircos.Ribbon.Plot(ribbon.data=RCircos.Ribbon.Data, track.num=11, by.chromosome=FALSE, twist=FALSE);

dev.off();

##由于R版本不同部分函数有差异

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