Merge branch 'master' of https://git.tunstall.in/tanu/LSHTM_analysis

scripts/functions/bp_lineage.R

@@ -5,9 +5,9 @@
 ########################################
 
 lin_count_bp <- function( lf_data = lin_lf
+                          , all_lineages = F
                           , x_categ = "sel_lineages"
                           , y_count = "p_count"
-                          , all_lineages = F
                           , use_lineages = c("L1", "L2", "L3", "L4")
                           , bar_fill_categ = "count_categ"
                           , display_label_col = "p_count"

scripts/functions/consurfP.R

@@ -238,12 +238,31 @@ wideP_consurf <- function(plotdf
   my_xlim = length(unique(plotdf[[xvar_colname]])); my_xlim
   ymin    = min(plotdf[[yvar_colname]]); ymin
   ymax    = max(plotdf[[yvar_colname]]); ymax
+  # DEBUG
+  # x_factor = as.factor(plotdf[[xvar_colname]])
+  # y_colour_factor = as.factor(plotdf[[yvar_colourN_colname]])
+  
+  # cat('XXXX THIS:', str(x_factor))
+  # 
+  # g = ggplot(plotdf, aes_string(x = x_factor)
+  #                            , y = yvar_colname
+  #                            , colour = y_colour_factor)
 
   g = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
                              , y = yvar_colname
                              , colour = sprintf("factor(%s)", yvar_colourN_colname)
                              ))
-  # "if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
+  # g = ggplot(plotdf, aes_string(x = "position")
+  #                               , y = "consurf_score"
+  #                               , colour = "consurf_colour_rev") 
+  # g = ggplot(plotdf, aes_string(x = "position")
+  #                               , y = "consurf_score"
+  #                               , colour = "consurf_colour_rev") 
+  
+  # DEBUG
+  #g0=g
+  
+  "if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
   if (plot_type == "bar"){
     g0 = g +
       geom_bar(stat = "identity")
@@ -266,9 +285,9 @@ wideP_consurf <- function(plotdf
                                 ))
     }else{
 
-    g0 = g0
+  g0 = g0
 
-    }
+  }
 
   #---------------------
   # add axis formatting

scripts/functions/lf_bp.R

@@ -8,7 +8,7 @@
 
 lf_bp <- function(lf_df = lf_duet
                   , p_title = "DUET-DDG"
-                  , colour_categ = "duet_outcome"
+                  , colour_categ = "outcome"
                   , x_grp = "mutation_info_labels"
                   , y_var = "param_value"
                   , facet_var = "param_type"

scripts/functions/logoP_snp.R

@@ -52,8 +52,8 @@ LogoPlotSnps <- function(plot_df
 
 {
   # handle funky omit_snp_count. DOES NOT WORK YET
-  if (class(omit_snp_count != 'numeric')){
+  if (class(omit_snp_count) != "numeric"){
-    omit_snp_count <- as.numeric(unlist(str_extract_all(thing, regex("[0-9]"))))
+    omit_snp_count <- as.numeric(unlist(str_extract_all(omit_snp_count, regex("[0-9]+"))))
   }
    ############################################
    # Data processing for logo plot for nsSNPS

scripts/functions/my_pairs_panel.R

@@ -40,7 +40,7 @@ my_corr_pairs <- function (corr_data_all
 
 ######################################################################
 my_pp = function (x, smooth = TRUE, scale = FALSE, density = TRUE, ellipses = TRUE, 
-          digits = 2, method = "pearson", pch = 20, lm = FALSE, cor = TRUE, 
+          digits = 2, method = "spearman", pch = 20, lm = FALSE, cor = TRUE, 
           jiggle = FALSE, factor = 2, hist.col = "cyan", show.points = TRUE, 
           rug = TRUE, breaks = "Sturges", cex.cor = 1, wt = NULL, smoother = FALSE, 
           stars = FALSE, ci = FALSE, alpha = 0.05, ...) 

scripts/functions/stability_count_bp.R

@@ -15,8 +15,8 @@ theme_set(theme_grey())
   ## ...opt args
 #==========================================================
 stability_count_bp <- function(plotdf
-         , df_colname = "duet_outcome"
+         , df_colname = ""
-         , leg_title = "DUET"
+         , leg_title = ""
          , ats = 25     # axis text size
          , als = 22     # axis label size
          , lts = 20     # legend text size