Mercurial > repos > iuc > deseq2
comparison deseq2.R @ 27:d027d1f4984e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
| author | iuc |
|---|---|
| date | Mon, 28 Jun 2021 05:14:25 +0000 |
| parents | de44f8eff84a |
| children | cd9874cb9019 |
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| 26:6a3a025714d3 | 27:d027d1f4984e |
|---|---|
| 65 "fit_type", "t", 1, "integer", | 65 "fit_type", "t", 1, "integer", |
| 66 "many_contrasts", "m", 0, "logical", | 66 "many_contrasts", "m", 0, "logical", |
| 67 "outlier_replace_off", "a", 0, "logical", | 67 "outlier_replace_off", "a", 0, "logical", |
| 68 "outlier_filter_off", "b", 0, "logical", | 68 "outlier_filter_off", "b", 0, "logical", |
| 69 "auto_mean_filter_off", "c", 0, "logical", | 69 "auto_mean_filter_off", "c", 0, "logical", |
| 70 "beta_prior_off", "d", 0, "logical" | 70 "beta_prior_off", "d", 0, "logical", |
| 71 "alpha_ma", "A", 1, "numeric" | |
| 71 ), byrow = TRUE, ncol = 4) | 72 ), byrow = TRUE, ncol = 4) |
| 72 opt <- getopt(spec) | 73 opt <- getopt(spec) |
| 73 | 74 |
| 74 # if help was asked for print a friendly message | 75 # if help was asked for print a friendly message |
| 75 # and exit with a non-zero error code | 76 # and exit with a non-zero error code |
| 198 main = paste("Histogram of p-values for", title_suffix) | 199 main = paste("Histogram of p-values for", title_suffix) |
| 199 ) | 200 ) |
| 200 text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA) | 201 text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA) |
| 201 legend("topright", fill = rev(colori), legend = rev(names(colori)), bg = "white") | 202 legend("topright", fill = rev(colori), legend = rev(names(colori)), bg = "white") |
| 202 } | 203 } |
| 203 plotMA(res, main = paste("MA-plot for", title_suffix), ylim = range(res$log2FoldChange, na.rm = TRUE)) | 204 plotMA(res, main = paste("MA-plot for", title_suffix), ylim = range(res$log2FoldChange, na.rm = TRUE), alpha = opt$alpha_ma) |
| 204 } | 205 } |
| 205 | 206 |
| 206 if (verbose) { | 207 if (verbose) { |
| 207 cat(paste("primary factor:", primary_factor, "\n")) | 208 cat(paste("primary factor:", primary_factor, "\n")) |
| 208 if (length(factors) > 1) { | 209 if (length(factors) > 1) { |