genelist_specific_profileplot: profile plot specific to a genelist
In sethiyap/FungalSporeAnalysis: Genomics data analysis of fungal spores.

Description Usage Arguments Value Author(s) Examples

View source: R/genelist_specific_profileplot.R

Profile plot for list of genes to be subsetted from genome feature file.

genelist_specific_profileplot(feature_txDb, bw_files, genelist = NULL,
  tss = TRUE, palette = "cream_brown", max_key = 6, min_key = 0,
  top_line = TRUE, ymax = 6, ymin = 1, log2 = TRUE,
  rename = FALSE, output = TRUE, output_name = "Sample")

`feature_txDb`	A TxDb object of gene feature file, generated by `GenomicFeatures::makeTxDbFromGFF()`
`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()`
`genelist`	A tibble with two columns `1. gene_id and 2.Expression value` without header, to subset genes from the feature file. `default:NULL`
`tss`	Logical, if TRUE plot 1kb up/downstream of start co-ordinate; if FALSE plot 1kb up/downstream of gene-body `default: TRUE`
`palette`	A character vector to choose sequential palette; white_green white_red white_blue cream_pink cream_brown cream_green `default: cream_brown`
`max_key`	Numeric, maximum limit of the color key.`default:6`
`min_key`	Numeric, mimimum limit of the color key.`default:0`
`top_line`	Logical, whether to plot profile with average signal as line plot at the top of plot. `default: TRUE`
`ymax`	Numeric, y-axis maximum limit for lineplot `default:6`
`ymin`	Numeric, y-axis minimum limit for lineplot `default:1`
`log2`	Logical, whether to plot profile as log-transformed or not.
`rename`	Logical, whether to remove characters after first `- OR _`, suitable for long names of bw objects.`default: FALSE`
`output`	Logical, to return a output of profile plot or not. `default: TRUE, with output_name,if FALSE; plot will be returned` ** Highly recommended to plot in outfile when .bw files are more than 2.
`output_name`	A character vector containing name of the output plot.`default:Sample`

Parallel plots of profiles(log2) for given gene lists, ordered by given expression value (high to low).

pooja sethiya

## Not run: 

 # 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 bw files as GRanges object
 pol2_veA_wt_spore <- rtracklayer::import.bw("pol2_veA_wt_spore_mix22_CACAGTTGGT_normalized_repeat.bw")
 TBP_veA_wt_spore <- rtracklayer::import.bw("TBP_veA_wt_spore_mix22_CAGTTGGT_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)

 # Load example gene_list file
 gene_list <- readr::read_delim(system.file("extdata/genesets/an_spore_pol2.txt" , package = "FungalSporeAnalysis"), delim="\t", col_names = FALSE)

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

 bw_files <- c("pol2_veA_wt_spore","TBP_veA_wt_spore")
 genelist_specific_profileplot(feature_txDb=feature_txDb,bw_files = bw_files, genelist=gene_list, output_name="An_Pol2_TBP_TFIIB", ymin=3)


## End(Not run)