j-andrews7

make.heatmaps <- function(dds, res, rld, level, g1, g2, plot_annos=NULL) {
    # plot_annos should be a vector of at least two columns from the sample sheet to use for labeling plots. 
    # g1 and g2 should be strings for the groups to be compared for the level (eg. "Progression", "Response")
    # dds must be a DESeqExperiment object.
    # rld is the log-transformed dds object.
    
    ## Should really make another generic function for the actual heatmap plots and feed it in the pval/lfc values.
    
    # Set color breaks and palatte.
    breaks <- c(seq(-3,-1.251,length=250),seq(-1.25,-0.1001,length=250),seq(-0.1,0.1,length=1),seq(0.1001,1.25,length=250),seq(1.251,3,length=250))

j-andrews7

j-andrews7

HANDY ONE-LINE SCRIPTS FOR AWK                               30 April 2008
Compiled by Eric Pement - eric [at] pement.org               version 0.27

Latest version of this file (in English) is usually at:
   http://www.pement.org/awk/awk1line.txt

This file will also be available in other languages:
   Chinese  - http://ximix.org/translation/awk1line_zh-CN.txt   

USAGE:

j-andrews7

FILE SPACING:

 # double space a file
 sed G

 # double space a file which already has blank lines in it. Output file
 # should contain no more than one blank line between lines of text.
 sed '/^$/d;G'

j-andrews7

add_clonotype <- function(tcr_location, seurat_obj){
    tcr <- read.csv(paste(tcr_folder,"filtered_contig_annotations.csv", sep=""))

    # Remove the -1 at the end of each barcode.
    # Subsets so only the first line of each barcode is kept,
    # as each entry for given barcode will have same clonotype.
    tcr$barcode <- gsub("-1", "", tcr$barcode)
    tcr <- tcr[!duplicated(tcr$barcode), ]

    # Only keep the barcode and clonotype columns.