Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.r @ 6:a3be3601bcb3 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
author artbio
date Mon, 09 Oct 2017 11:07:09 -0400
parents 12c14642e6ac
children a96e6a7df2b7
comparison
equal deleted inserted replaced
5:12c14642e6ac 6:a3be3601bcb3
10 library(optparse) 10 library(optparse)
11 11
12 option_list <- list( 12 option_list <- list(
13 make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"), 13 make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"),
14 make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"), 14 make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"),
15 make_option(c("-n", "--normalization"), type="character", help="space-separated normalization/size factors"),
15 make_option("--first_plot_method", type = "character", help="How additional data should be plotted"), 16 make_option("--first_plot_method", type = "character", help="How additional data should be plotted"),
16 make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"), 17 make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"),
17 make_option("--output_pdf", type = "character", help="path to the pdf file with plots") 18 make_option("--output_pdf", type = "character", help="path to the pdf file with plots")
18 ) 19 )
19 20
25 Table = read.delim(args$first_dataframe, header=T, row.names=NULL) 26 Table = read.delim(args$first_dataframe, header=T, row.names=NULL)
26 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") { 27 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") {
27 Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) 28 Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
28 } 29 }
29 n_samples=length(unique(Table$Dataset)) 30 n_samples=length(unique(Table$Dataset))
31 samples = unique(Table$Dataset)
32 if (args$normalization != "") {
33 norm_factors = as.numeric(unlist(strsplit(args$normalization, " ")))
34 } else {
35 norm_factors = rep(1, n_samples)
36 }
37 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size" | args$first_plot_method == "Coverage") {
38 i = 1
39 for (sample in samples) {
40 print(norm_factors[i])
41 Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i]
42 i = i + 1
43 }
44 print(tail(Table))
45 }
30 genes=unique(levels(Table$Chromosome)) 46 genes=unique(levels(Table$Chromosome))
31 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x)) 47 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
32 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) ) 48 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
33 n_genes=length(per_gene_readmap) 49 n_genes=length(per_gene_readmap)
34 # second table 50 # second table
35 if (args$extra_plot_method != '') { 51 if (args$extra_plot_method != '') {
36 ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL) 52 ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
37 if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') { 53 if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') {
38 ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1)) 54 ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
39 } 55 }
56 if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size" | args$extra_plot_method == "Coverage") {
57 i = 1
58 for (sample in samples) {
59 ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample] <- ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample]*norm_factors[i]
60 i = i + 1
61 }
62 }
40 per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x)) 63 per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x))
41 } 64 }
42 65
43 ## functions 66 ## functions
44 67
45 plot_unit = function(df, method=args$first_plot_method, ...) { 68 plot_unit = function(df, method=args$first_plot_method, ...) {
46 if (method == 'Counts') { 69 if (method == 'Counts') {