lineplot for bw file — lineplot_for_bw • FungalSporeAnalysis

Plot line-plot of each percentile for given gene-list.

lineplot_for_bw(feature_txDb, genelist, bw_file, output_name = "Sample",
  tss = "TRUE", expression_value = TRUE, tiles = 4, median = TRUE)

Arguments

feature_txDb	A TxDb object of gene feature file, generated by `GenomicFeatures::makeTxDbFromGFF()`
genelist	A tibble with two columns `1. gene_id and 2.Expression value or Percentile rank` without header, to subset genes from the feature file.
output_name	A character vector containing name of the output plot.`default:Sample`
tss	Logical, if TRUE plot 1kb up/downstream of start co-ordinate; if FALSE plot 1kb up/downstream of gene-body `default: TRUE`
expression_value	Logical, if TRUE percentile is calculated based on the expression value column (ie. second column), if FALSE second column should define the percentiles. `default: TRUE`
tiles	Numeric, when `expression_value=TRUE`, specify the number of percentiles inorder to divide the data.`default: 4`
median	Logical, to display median or mean line of percentiles.`default: TRUE`
bw_files	A character vector containing either name or names of GRanges object of bw or bdg files. GRanges object for bw_files can be generated by: `rtracklayer::import()`

Value

A line-plot of percentiles and a tibble of percentiles appended to expression data.

Examples


if (FALSE) {

 # Load feature file from system data, to run example data
 feature_txDb <- AnnotationDbi::loadDb(system.file("extdata/sqllite/an_feature_file_s10_m04_r07.sqlite" , package = "FungalSporeAnalysis"))

 # Or load feature file as TxDb
 feature_txDb <- GenomicFeatures::makeTxDbFromGFF("an_feature_file_s10_m04_r07.gff")

 # load list of genes to subset from all the genes
 genelist_dat <- system.file("extdata/genesets/an_spore_pol2_for_percentilelineplot.txt" , package = "FungalSporeAnalysis")
 genelist <- readr::read_delim(genelist_dat,delim="\t", col_names=FALSE)

 # Load bw files as GRanges object
 pol2_veA_wt_spore <- rtracklayer::import.bw("pol2_veA_wt_spore_mix22_CACAGTTGGT_normalized_repeat.bw")

 # Load GRanges object from system data, to run example data
 data_files <- system.file("extdata/sysdata.rda" , package = "FungalSporeAnalysis")
 load(data_files)

 ###########################################

 lineplot_for_bw(feature_txDb, genelist =genelist,bw_file="pol2_veA_wt_spore", output_name = "pol2_veA_wt_spore")

}