In jinhyunju/icreport: Tools for creating a visual summary of matrix decomposition results.

Component Visualization Report

• Generated with R package icreport

# setting global options 
figure.outpath <- paste(output.path,"/icreport_figures/",prefix,"/",sep="")
opts_chunk$set(fig.path=figure.outpath,dev=file.ext, warning=FALSE, message=FALSE)
options(warn=-1,width = 100)
flower.palette <- c("#283545","#E09E12","#A72613","#95CDDC","#395717","#3A3B35","#D68931","#442243")

cat(toupper(attr(input_list, "method")), " Analysis Report \n")
cat("Dataset = ", prefix,"\n")

Individual Component Information

for( i in 1:n_comps){
    ###################### Plotting without Gene information ########################## 
    # check if there is a specified order for the ICs (default is by explained variance)
    p <- order(input_list$percent_var, decreasing = TRUE)[i]


    cat("------------------------------------------------------------------------------","\n")

    ic.info <- data.frame("plot_number" = i,
                          "Variance_Percent" = input_list$percent_var[p])
    print(ic.info)

    cat("------------------------------------------------------------------------------","\n")

    plot_single_component(input_list, comp_idx = p, geneinfo_df = geneinfo_df)



}

jinhyunju/icreport documentation built on May 19, 2019, 10:35 a.m.