version 1.8

DESCRIPTION

@@ -1,11 +1,14 @@
 Package: hciR
 Title: RNA-seq workflows at HCI
-Version: 1.7
+Version: 1.8
 Author: Chris Stubben
 Maintainer: Chris Stubben <[email protected]>
+Depends:
+    R (>= 2.10)
 Imports:
     dplyr,
     readr,
+    readxl,
     tidyr,
     tibble,
     magrittr,
@@ -30,5 +33,6 @@ License: GPL-3
 Encoding: UTF-8
 Description: This package simplifies the R code in a differential expression analysis for markdown reports. The package includes functions to run DESeq2 using sample and count tibbles as input, get annotated DESeq results for all pairwise comparisons and create interactive plots and other visualizations.
 LazyData: true
+LazyDataCompression: xz
 biocViews: Software
 RoxygenNote: 7.3.1

NAMESPACE

@@ -7,7 +7,6 @@ export(as_tbl)
 export(check_contrasts)
 export(deseq_from_tibble)
 export(drop_empty_columns)
-export(enricher_all)
 export(extract_samples)
 export(fgsea_all)
 export(filter_counts)
@@ -20,11 +19,9 @@ export(palette255)
 export(plot_biotypes)
 export(plot_counts)
 export(plot_dist)
-export(plot_enricher)
 export(plot_fgsea)
 export(plot_filter)
 export(plot_genes)
-export(plot_gsea)
 export(plot_interactions)
 export(plot_ma)
 export(plot_pca)

R/plot_counts.R

@@ -17,7 +17,8 @@
 #' @author Chris Stubben
 #'
 #' @examples
-#'  plot_counts(pasilla$count, "FBgn0033635",  c("type","condition"), title = "Prip")
+#'  x <- top_counts(pasilla$results, pasilla$rlog, top=12)
+#'  plot_counts(x, "condition")
 #' @export
 
 plot_counts <- function(x, intgroup, n=25, geom="jitter", ylab = "Log2 counts", reorder, ncol=NULL, scales="fixed", ...){
@@ -32,7 +33,7 @@ plot_counts <- function(x, intgroup, n=25, geom="jitter", ylab = "Log2 counts",
       x1 <- x1[, 1:n]
   }
   y <- data.frame(s1[, intgroup, drop=FALSE], x1)
-  z <- tidyr::gather(y, -all_of(intgroup), key="gene2", value = "count")
+  z <- tidyr::gather(y, -dplyr::all_of(intgroup), key="gene2", value = "count")
    ## reorder?
    if(!missing(reorder)) z[[1]] <- factor(z[[1]], levels = reorder)
 

R/plot_interactions.R

@@ -6,6 +6,7 @@
 #' @param ylab y-axis label
 #' @param scaled scale counts
 #' @param n total number of genes to plot
+#' @param max_scale maximum values for scaled values in case of outliers
 #' @param reorder level names to reorder factor levels on x-axis
 #' @param \dots additional options like ncol or nrow passed to facet_wrap
 #'
@@ -14,7 +15,7 @@
 #' @author Chris Stubben
 #'
 #' @examples
-#'  x <- top_counts( pasilla$res, pasilla$rlog, top=25)
+#'  x <- top_counts( pasilla$results, pasilla$rlog, top=25)
 #'  # no interaction from single or paired end as expected
 #'  plot_interactions(x,  c("condition", "type"))
 #' @export

R/read_deseq.R

@@ -24,12 +24,12 @@ read_deseq <- function(file,  object="results"){
       names(res) <- gsub("_vs_", " vs. ", wk[n])
       for(i in seq_along(n))  {
           message("Loading ", names(res)[i])
-          res[[i]] <- read_excel(file, sheet= n[i])
+          res[[i]] <- readxl::read_excel(file, sheet= n[i])
       }
    } else{
       s1 <- readxl::read_excel(file, sheet="samples")
       message("Loading ", object, " worksheet")
-      r1 <- read_excel(file, sheet= object)
+      r1 <- readxl::read_excel(file, sheet= object)
       ## delete gene_name and biotype
       n2 <- which(colnames(r1) %in% c("gene_name", "biotype"))
       if(length(n2) !=2) message("Note: Gene name and biotype columns are missing?")