fixed pos_count cals in function by specifying dplyr and changed summarize to summarise

scripts/functions/my_pairs_panel.R

@@ -38,14 +38,6 @@ my_corr_pairs <- function (corr_data_all
   
 }
 
-c_plot <- my_corr_pairs(corrplot_df
-                        
-                        , dot_size = 1.6
-                        , ats = 1.5
-                        , corr_lab_size = 1.5
-                        , corr_value_size = 1)
-
-
 ######################################################################
 my_pp = function (x, smooth = TRUE, scale = FALSE, density = TRUE, ellipses = TRUE, 
           digits = 2, method = "pearson", pch = 20, lm = FALSE, cor = TRUE, 

scripts/functions/position_count_bp.R

@@ -42,7 +42,9 @@ site_snp_count_bp <- function (plotdf
              , "\nNo. of cols:", ncol(plotdf)
              , "\nNow adding column: frequency of mutational positions"))
   
-  # adding snpcount for each position 
+  #-------------------------------------------
+  # adding column: snpcount for each position 
+  #-------------------------------------------
   setDT(plotdf)[, pos_count := .N, by = .(eval(parse(text = df_colname)))] 
 
   cat("\nCumulative nssnp count\n"
@@ -65,13 +67,18 @@ site_snp_count_bp <- function (plotdf
              , "\nNo. of rows:", nrow(plotdf)
              , "\nNo. of cols:", ncol(plotdf)))
 
+  #------------------------------------------------------
+  # creating df: average count of snpcount for each position 
+  # created in earlier step
+  #-------------------------------------------------------
   # use group by on pos_count
   snpsBYpos_df <- plotdf %>%
-    group_by(eval(parse(text = df_colname))) %>%
-    summarize(snpsBYpos = mean(pos_count))
+    dplyr::group_by(eval(parse(text = df_colname))) %>%
+    dplyr::summarise(snpsBYpos = mean(pos_count)) # changed from summarize!
   
-  cat("\nnssnp count\n"
-      , table(snpsBYpos_df$snpsBYpos))
+  cat("\nnssnp count per position\n"
+      , table(snpsBYpos_df$snpsBYpos)
+      , "\n")
 
   # calculating total no. of sites associated with nsSNPs
   tot_sites = sum(table(snpsBYpos_df$snpsBYpos))

scripts/plotting/Header_TT.R

@@ -6,7 +6,6 @@
 #########################################################
 #lib_loc = "/usr/local/lib/R/site-library")
 
-
 require("getopt", quietly = TRUE) # cmd parse arguments
 
 if (!require("tidyverse")) {
@@ -19,6 +18,11 @@ if (!require("shiny")) {
   library(shiny)
 }
 
+if (!require("shinyBS")) {
+  install.packages("shinyBS", dependencies = TRUE)
+  library(shinyBS)
+}
+
 if (!require("gridExtra")) {
   install.packages("gridExtra", dependencies = TRUE)
   library(gridExtra)
@@ -39,6 +43,11 @@ if (!require("ggridges")) {
 #   library(dplyr)
 # }
 
+if (!require ("DT")){
+  install.packages("DT")
+  library(DT)
+}
+
 if (!require ("plyr")){
    install.packages("plyr")
    library(plyr)