Commit 23d21d5c authored by Holger Brandl's avatar Holger Brandl

added NA support for gene info; upscaled MA plots to more contrasts

parent 3fdacd26
......@@ -258,7 +258,8 @@ summary(dt) %>% as_df %>% kable
#' plot MA per contrast
numContrasts = length(colnames(tfit))
par(mfrow = c(1, numContrasts)) ## 2panel plot for mean-var relationship before and after boom
par(mfrow=c(1,1))
# par(mfrow = c(4, numContrasts)) ## 2panel plot for mean-var relationship before and after boom
# colnames(tfit) %>% iwalk(~ plotMD(tfit, column=.y, status=dt[,.y], main=.x, xlim=c(-8,13)))
colnames(tfit) %>% iwalk(~ plotMD(tfit, column = .y, status = dt[, .y], main = .x))
......@@ -361,8 +362,14 @@ if (is.null(gene_info_file)) {
# geneLengths = transmute(geneInfo, gene_id, gene_length = end_position - start_position)
geneDescs = transmute(geneInfo, gene_id, gene_name = external_gene_name, gene_description = description)
} else {
geneInfo = read_tsv(gene_info_file)
colnames(geneInfo)[1] = "gene_id"
if(gene_info_file != "NA"){
geneInfo = read_tsv(gene_info_file)
colnames(geneInfo)[1] = "gene_id"
}else{
# no info --> create dummy info
geneInfo = distinct(countData, gene_id)
}
geneDescs = geneInfo
}
......
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