update new mapper

R/doGSEA.R

@@ -144,16 +144,25 @@ L2FC <- function(mat, l1, l2, method="t", eps=0) {
 #' @param stana stana object
 #' @param candSp candidate species ID
 #' @param how how to summarize multiple gene CN assigned to the same KO
+#' @param annot eggNOG or manual
 #' @export
-calcKO <- function(stana, candSp=NULL, how=sum) {
+calcKO <- function(stana, candSp=NULL, how=sum, annot="eggNOG") {
 	checkID(stana, candSp)
     if (is.null(candSp)) {cat("Species not specified, the first ID will be used:", stana@ids[1]);
         candSp <- stana@ids[1]
     }
-    if (is.null(stana@eggNOG[[candSp]])) {stop("Please provide list of path to annotation file by `setAnnotation` function.")}
-    ko_df_filt <- summariseAbundance(stana, sp = candSp,
-        checkEGGNOG(annot_file=stana@eggNOG[[candSp]], "KEGG_ko"),
-        how=how)
+    if (annot=="eggNOG") {
+	    if (is.null(stana@eggNOG[[candSp]])) {stop("Please provide list of path to annotation file by `setAnnotation` function.")}
+	    ko_df_filt <- summariseAbundance(stana, sp = candSp,
+	        checkEGGNOG(annot_file=stana@eggNOG[[candSp]], "KEGG_ko"),
+	        how=how)    	
+    } else {
+    	if (is.null(stana@map[[candSp]])) {stop("Please set mapping data.frame in map slot using `setMap`.")}
+	    ko_df_filt <- summariseAbundance(stana, sp = candSp,
+	        stana@map[[candSp]],
+	        how=how)
+    }
+
     stana@kos[[candSp]] <- ko_df_filt
     stana
 }

R/stana.R

@@ -8,6 +8,7 @@
 #' @slot kos stores ko table
 #' @slot type type of pipeline, such as `MIDAS`
 #' @slot eggNOG list of path for eggNOG mapper v2 results for species
+#' @slot map slot storing the mapping data.frame for gene ID and orthology
 setClass("stana", slots=list(
                             type="character",
                             cl="list",
@@ -45,7 +46,8 @@ setClass("stana", slots=list(
                             colors="vector",
                             geneCluster="list",
                             paFilterUp="numeric",
-                            paFilterDown="numeric"))
+                            paFilterDown="numeric",
+                            map="list"))
 setMethod("show",
   signature(object="stana"),
   function(object) {
@@ -155,6 +157,23 @@ setAnnotation <- function(stana, annotList) {
 	return(stana)
 }
 
+
+#' setMap
+#' @param stana stana object
+#' @param candSp species ID
+#' @param map mapping data.frame, two column consisting of ID and value.
+#' The function internally changes the column name.
+#' ID is gene ID in `genes` slot, and value indicates orthology ID (like K00001)
+#' @export
+#' @return stana object
+setMap <- function(stana, candSp, map) {
+	if (dim(map)[2]!=2) {stop("Please provide two-column data.frame")}
+	colnames(map) <- c("ID", "value")
+	stana@map[[candSp]] <- map
+	return(stana)
+}
+
+
 #' getColors
 #' @import RColorBrewer
 #' @noRd

README.Rmd

@@ -71,9 +71,12 @@ stana <- stana |>
   inferAndPlotTree(meta=c("treatment","marker"))
 getFasta(stana)[[1]]
 getTree(stana)[[1]]
-getSlot(stana, "treePlotList")[[1]]
+getTreePlot(stana)[[1]]
 ```
 
+If the gene copy number table is available like in `MIDAS` series and `inStrain`, one can compare the functional implications of these gene contents.
+
+
 ## Interactive inspection
 
-The users can inspect metagenotyping results interactively using Shiny based on the variables such as disease conditions (`exportInteractive()`).
+The users can inspect metagenotyping results interactively using Shiny based on the variables such as disease conditions (`exportInteractive()`). One can publish the results in the hosting services for sharing the research findings.

README.md

@@ -69,7 +69,7 @@ stana <- setMetadata(stana, metadata)
 ## Infer and plot tree based on metadata
 stana <- stana |>
   consensusSeq(argList=list(site_prev=0.95)) |>
-  plotTree(meta=c("treatment","marker"))
+  inferAndPlotTree(meta=c("treatment","marker"))
 #> Beginning calling for 100003
 #>   Site number: 5019
 #>   Profiled samples: 11
@@ -85,7 +85,7 @@ getTree(stana)[[1]]
 #>   ERR1711593, ERR1711594, ERR1711596, ERR1711598, ERR1711603, ERR1711605, ...
 #> 
 #> Unrooted; includes branch lengths.
-getSlot(stana, "treePlotList")[[1]]
+getTreePlot(stana)[[1]]
 ```
 
 <img src="man/figures/README-unnamed-chunk-2-1.png" width="1800" style="display: block; margin: auto;" />