Merge branch 'version2.0.1'

pendy05 · Nov 22, 2024 · c00e62b · c00e62b
2 parents 25f50aa + 0ec334f
commit c00e62b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: vDiveR
 Type: Package
 Title: Visualization of Viral Protein Sequence Diversity Dynamics
-Version: 2.0.0
+Version: 2.0.1
 Authors@R: c(
     person("Pendy", "Tok", email = "[email protected]", role = c("aut", "cre")),
     person("Li Chuin", "Chong", role = "aut"),
@@ -22,18 +22,18 @@ Imports:
     ggplot2,
     ggpubr,
     grid,
-    gridExtra,
     ggtext,
     magrittr,
-    plyr,
     tidyr,
     stringr,
     rlang,
     rentrez,
     scales,
     utils,
-    maps
-RoxygenNote: 7.3.1
+    maps,
+    cowplot,
+    stringdist
+RoxygenNote: 7.3.2
 Depends:
     R (>= 2.10)
 Suggests:

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,24 +3,27 @@
 export(concat_conserved_kmer)
 export(json2csv)
 export(metadata_extraction)
-export(plot_conservationLevel)
+export(plot_conservation_level)
 export(plot_correlation)
 export(plot_dynamics_protein)
 export(plot_dynamics_proteome)
 export(plot_entropy)
 export(plot_time)
-export(plot_worldmap)
+export(plot_world_map)
+importFrom(cowplot,plot_grid)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
 importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,if_else)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_if)
 importFrom(dplyr,n)
 importFrom(dplyr,right_join)
+importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
@@ -77,10 +80,7 @@ importFrom(ggpubr,ggarrange)
 importFrom(ggpubr,text_grob)
 importFrom(ggtext,geom_richtext)
 importFrom(grid,unit)
-importFrom(gridExtra,grid.arrange)
 importFrom(magrittr,"%>%")
-importFrom(plyr,.)
-importFrom(plyr,ddply)
 importFrom(rentrez,entrez_fetch)
 importFrom(rentrez,entrez_search)
 importFrom(rlang,":=")
@@ -89,6 +89,7 @@ importFrom(scales,math_format)
 importFrom(scales,trans_breaks)
 importFrom(scales,trans_format)
 importFrom(stats,aggregate)
+importFrom(stringdist,stringdist)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_sub)
 importFrom(stringr,str_to_title)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,6 @@
-# vDiveR 2.0.0
+# vDiveR 2.0.1
 
 - Added a `NEWS.md` file to track changes to the package.
 
-* Refactored metadata code and vDiveR currently handles DiMA of version 5.0.9.
+* Refactored metadata code and vDiveR currently handles DiMA of version 5.0.9.
+* Fixed bugs: plot parameters, plot display (such as legend), world map region handling.
diff --git a/R/json2csv.R b/R/json2csv.R
@@ -70,7 +70,8 @@ json2csv <-function(json_data, host_name="unknown host", protein_name="unknown p
     colnames(motifs)<-c('position','index.incidence','major.incidence','minor.incidence','unique.incidence','multiIndex','proteinName','count','lowSupport','entropy','distinctVariant.incidence','totalVariants.incidence','indexSequence','highestEntropy.position','highestEntropy','averageEntropy','host')
     #reorder the columns
     motifs<-motifs[,c(7,1,8,9,10,13,2,3,4,5,12,11,6,17,14,15,16)]
-
+    #assign protein name
+    motifs['proteinName'] <- protein_name
     motifs
 
 }

diff --git a/R/metadata_extraction.R b/R/metadata_extraction.R
@@ -1,4 +1,4 @@
-#' Metadata Extraction from NCBI/GISAID EpiCoV FASTA file
+#' Metadata Extraction from NCBI/GISAID (EpiFlu/EpiCoV/EpiPox/EpiArbo) FASTA file
 #'
 #' This function retrieves metadata (ID, region, date) from the input FASTA file, with the source of, either 
 #' NCBI (with default FASTA header) or GISAID (with default FASTA header). The function will return a dataframe