## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( fig.align = "center", fig.width = 3, fig.height = 3, collapse = TRUE, warning = FALSE, message = FALSE ) library(grid) library(plotgardener) library(plotgardenerData) ## ----hic_quickplot, eval=TRUE, echo=TRUE, message=FALSE----------------------- ## Load plotgardener library(plotgardener) ## Load example Hi-C data library(plotgardenerData) data("IMR90_HiC_10kb") ## Quick plot Hi-C data plotHicSquare( data = IMR90_HiC_10kb, chrom = "chr21", chromstart = 28000000, chromend = 30300000, assembly = "hg19" ) ## ----signal_quickplot, eval=TRUE, echo=TRUE, message=FALSE-------------------- ## Load plotgardener library(plotgardener) ## Load example signal data library(plotgardenerData) data("IMR90_ChIP_H3K27ac_signal") ## Quick plot signal data plotSignal( data = IMR90_ChIP_H3K27ac_signal, chrom = "chr21", chromstart = 28000000, chromend = 30300000, assembly = "hg19" ) ## ----gene_quickplot, eval=TRUE, echo=TRUE, message=FALSE---------------------- ## Load plotgardener library(plotgardener) ## Load hg19 genomic annotation packages library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) ## Quick plot genes plotGenes( assembly = "hg19", chrom = "chr21", chromstart = 28000000, chromend = 30300000 ) ## ----gwas_quickplot, eval=TRUE, echo=TRUE, message=FALSE---------------------- ## Load plotgardener library(plotgardener) ## Load hg19 genomic annotation packages library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## Load example GWAS data library(plotgardenerData) data("hg19_insulin_GWAS") ## Quick plot GWAS data plotManhattan( data = hg19_insulin_GWAS, assembly = "hg19", fill = c("steel blue", "grey"), ymax = 1.1, cex = 0.20 ) ## ----quickpage, echo=TRUE, fig.height=4, fig.width=4, message=FALSE----------- pageCreate(width = 3.25, height = 3.25, default.units = "inches") ## ----eval=FALSE, echo=TRUE, message=FALSE------------------------------------- # data("IMR90_HiC_10kb") # hicPlot <- plotHicSquare( # data = IMR90_HiC_10kb, # chrom = "chr21", chromstart = 28000000, chromend = 30300000, # assembly = "hg19", # x = 0.25, y = 0.25, width = 2.5, height = 2.5, default.units = "inches" # ) ## ----quickpageHic, echo=FALSE, fig.height=4, fig.width=4, message=FALSE------- pageCreate(width = 3.25, height = 3.25, default.units = "inches") data("IMR90_HiC_10kb") hicPlot <- plotHicSquare( data = IMR90_HiC_10kb, chrom = "chr21", chromstart = 28000000, chromend = 30300000, assembly = "hg19", x = 0.25, y = 0.25, width = 2.5, height = 2.5, default.units = "inches" ) ## ----eval=FALSE, echo=TRUE, message=FALSE------------------------------------- # annoHeatmapLegend( # plot = hicPlot, # x = 2.85, y = 0.25, width = 0.1, height = 1.25, default.units = "inches" # ) # # annoGenomeLabel( # plot = hicPlot, # x = 0.25, y = 2.75, width = 2.5, height = 0.25, default.units = "inches" # ) ## ----quickpageAnno, echo=FALSE, fig.height=4, fig.width=4, message=FALSE------ pageCreate(width = 3.25, height = 3.25, default.units = "inches") data("IMR90_HiC_10kb") hicPlot <- plotHicSquare( data = IMR90_HiC_10kb, chrom = "chr21", chromstart = 28000000, chromend = 30300000, assembly = "hg19", x = 0.25, y = 0.25, width = 2.5, height = 2.5, default.units = "inches" ) annoHeatmapLegend( plot = hicPlot, x = 2.85, y = 0.25, width = 0.1, height = 1.25, default.units = "inches" ) annoGenomeLabel( plot = hicPlot, x = 0.25, y = 2.75, width = 2.5, height = 0.25, default.units = "inches" ) ## ----eval=FALSE, echo=TRUE, message=FALSE------------------------------------- # pageGuideHide() ## ----quickpageHide, echo=FALSE, fig.height=4, fig.width=4, message=FALSE------ pageCreate( width = 3.25, height = 3.25, default.units = "inches", xgrid = 0, ygrid = 0, showGuides = FALSE ) data("IMR90_HiC_10kb") hicPlot <- plotHicSquare( data = IMR90_HiC_10kb, chrom = "chr21", chromstart = 28000000, chromend = 30300000, assembly = "hg19", x = 0.25, y = 0.25, width = 2.5, height = 2.5, default.units = "inches" ) annoHeatmapLegend( plot = hicPlot, x = 2.85, y = 0.25, width = 0.1, height = 1.25, default.units = "inches" ) annoGenomeLabel( plot = hicPlot, x = 0.25, y = 2.75, width = 2.5, height = 0.25, default.units = "inches" ) ## ----eval=FALSE, echo=TRUE, message=FALSE------------------------------------- # pdf(width = 3.25, height = 3.25) # # pageCreate(width = 3.25, height = 3.25, default.units = "inches") # data("IMR90_HiC_10kb") # hicPlot <- plotHicSquare( # data = IMR90_HiC_10kb, # chrom = "chr21", chromstart = 28000000, chromend = 30300000, # assembly = "hg19", # x = 0.25, y = 0.25, width = 2.5, height = 2.5, default.units = "inches" # ) # annoHeatmapLegend( # plot = hicPlot, # x = 2.85, y = 0.25, width = 0.1, height = 1.25, default.units = "inches" # ) # # annoGenomeLabel( # plot = hicPlot, # x = 0.25, y = 2.75, width = 2.5, height = 0.25, default.units = "inches" # ) # pageGuideHide() # # dev.off() ## ----------------------------------------------------------------------------- sessionInfo()