Merge pull request #75 from PNNL-Comp-Mass-Spec/develop_damon

Develop damon

R/colorschemes.R

@@ -140,6 +140,7 @@ NULL
 
 
 
+
 #' @export blue.colors
 #' @describeIn colorschemes based on RColorBrewer "Blues"
 blue.colors <- function(n)

R/complex_heatmap.R

@@ -117,7 +117,7 @@
 #' complex_heatmap(ee)
 #'
 #' # Limit color range to see differences more easily
-#' complex_heatmap(ee, color_range = c(-2, 2))
+#' complex_heatmap(ee, color_range = c(-2, 0, 2))
 #'
 #' # Sample correlation heatmap
 #' complex_heatmap(ee, heatmap_type = "s")

R/read_FragPipe_LFQ.R

@@ -15,9 +15,11 @@
 #' @importFrom dplyr %>% select filter distinct relocate everything mutate
 #'
 #' @examples
+#' \dontrun{
 #' file_path <- "C:/Users/fakeusr222/Desktop/MSF_LFQ_job/MSstats.csv"
-#'   msnset <- read_FragPipe_LFQ(file_path)
-#'   show(msnset)
+#' msnset <- read_FragPipe_LFQ(file_path)
+#' show(msnset)
+#' }
 #'
 #' @export read_FragPipe_LFQ
 

R/read_FragPipe_TMT.R

@@ -6,7 +6,7 @@
 #'
 #' @param path character; File path to the desired FragPipe-generated tmt-report file.
 #'   Any tmt-report file may be used.
-#' @org_to_retain character; Filtering out contaminants. The argument is the
+#' @param org_to_retain character; Filtering out contaminants. The argument is the
 #'   official organism name such as "Homo sapiens" or "Bos taurus" or
 #'   "Sus scrofa". Default is NULL, meaning pass all.
 #' @param use_gene_as_prot_id logical; Used only in case of `single-site` files. Switches
@@ -22,9 +22,11 @@
 #' @importFrom dplyr %>% select mutate
 #'
 #' @examples
+#' \dontrun{
 #' file_path <- "C:/Users/fakeusr222/Desktop/MSF_TMT_job/ratio_multi-site_MD.tsv"
 #'   msnset <- read_FragPipe_TMT(file_path)
 #'   show(msnset)
+#' }
 #'
 #' @export read_FragPipe_TMT
 

vignettes/complex_heatmap.Rmd

@@ -42,7 +42,7 @@ complex_heatmap(ee)
 Due to the wide range of values, it is difficult to see color differences. We can fix this by setting limits on the range of the color scale. This does not affect the actual data: just the colors of the heatmap body. We will limit colors to (-1.5, 1.5). Values below -1.5 will be the same shade of blue, and values above 1.5 will be the same shade of red.
 
 ```{r}
-complex_heatmap(ee, color_range = c(-1.5, 1.5))
+complex_heatmap(ee, color_range = c(-1.5, 0, 1.5))
 ```
 
 

vignettes/id_conversion.Rmd

@@ -81,7 +81,7 @@ bitr(genes, fromType="SYMBOL", toType="UNIPROT", OrgDb="org.Hs.eg.db")
 This one may or may not to work.  There some persistent troubles due to [BioMart 
 site migration](http://www.biomart.org/news.html).  
 When it works, it is really great, though.
-```{r biomartm, message=FALSE}
+```{r biomartm, message=FALSE, eval = FALSE}
 library(biomaRt)
 # listMarts()
 ensembl <- useMart("ensembl")