easier select_haplo

NAMESPACE

@@ -10,6 +10,7 @@ import(purrr)
 import(shiny)
 import(shinyWidgets)
 import(shinydashboard)
+import(tidyr)
 import(vroom)
 importFrom(JBrowseR,JBrowseR)
 importFrom(JBrowseR,JBrowseROutput)
@@ -33,6 +34,7 @@ importFrom(grDevices,col2rgb)
 importFrom(grDevices,hcl)
 importFrom(grDevices,hsv)
 importFrom(grDevices,rgb2hsv)
+importFrom(graphics,legend)
 importFrom(hidecan,CAN_data)
 importFrom(hidecan,DE_data)
 importFrom(hidecan,GWAS_data)

R/functions_map.R

@@ -19,6 +19,7 @@
 #' @param software character defined from each software it comes from
 #' 
 #' @return graphic representing selected section of a linkage group
+#' @importFrom  graphics legend
 #' 
 #' @keywords internal
 draw_map_shiny<-function(left.lim = 0, right.lim = 5, ch = 1,

R/functions_qtl.R

@@ -766,6 +766,7 @@ plot.mappoly.homoprob <- function(x, stack = FALSE, lg = NULL,
 #' 
 #' @return ggplot graphic
 #' 
+#' @import dplyr tidyr
 #' 
 #' @keywords internal
 select_haplo <- function(input.haplo,probs, selected_mks, effects.data, exclude.haplo = NULL){
@@ -788,7 +789,7 @@ select_haplo <- function(input.haplo,probs, selected_mks, effects.data, exclude.
   subset <- homo.dat$homoprob[which(data_match %in% include),]
   subset <- subset[which(subset$probability > 0.5),]
 
-  counts <- subset %>% group_by(marker, individual, LG) %>% summarise(n = n())
+  counts <- subset %>% group_by(individual) %>% summarise(n = n())
   selected <- counts$individual[counts$n == length(input.haplo)]
 
   if(length(selected) == 0) stop("None of the inviduals have these combination of haplotypes")