feat: clonality init

NAMESPACE

@@ -4,6 +4,7 @@ export("%>%")
 export(get_study)
 export(plot_motif_counts)
 exportClasses(Basic)
+exportClasses(Clonality)
 exportClasses(Diversity)
 exportClasses(Motif)
 exportClasses(reTCRProj)

R/get_study.R

@@ -1,5 +1,6 @@
 source("R/utils-basic.R")
 source("R/utils-diversity.R")
+source("R/utils-clonality.R")
 
 #' Get pyTCR data of a project
 #'
@@ -23,11 +24,13 @@ get_study <- function(id, attr_col) {
 
   basic <- .get_basic(data = data, attr_col = attr_col)
   diversity <- .get_diversity(data = data, attr_col = attr_col)
+  clonality <- .get_clonality(data = data, attr_col = attr_col)
 
   return(methods::new(
     "reTCRProj",
     data = data,
     basic = basic,
-    diversity = diversity
+    diversity = diversity,
+    clonality = clonality
   ))
 }

R/retcr_proj_class.R

@@ -1,6 +1,6 @@
 #' Class "Basic"
 #'
-#' A class to represent basic analysis data.
+#' A class to represent basic metrics
 #'
 #' @slot summary_data summary data
 #' @slot reads_count read counts
@@ -24,25 +24,9 @@ setClass("Basic",
   )
 )
 
-#' Class "Motif"
-#'
-#' A class to represent motif data.
-#'
-#' @slot aa_spectratype aa spectratype data.
-#' @slot aa_max_spectratype aa max spectratype data.
-#' @slot aa_motif_count aa motif count data.
-#' @exportClass Motif
-setClass("Motif",
-  slots = c(
-    aa_spectratype = "data.frame",
-    aa_max_spectratype = "data.frame",
-    aa_motif_count = "data.frame"
-  )
-)
-
 #' Class "Diversity"
 #'
-#' A class to represent diversity data.
+#' A class to represent diversity metrics
 #'
 #' @slot shannon Shannon-Wiener indexes
 #' @slot simpson Simpson indexes
@@ -60,18 +44,60 @@ setClass("Diversity",
   )
 )
 
+#' Class "Clonality"
+#'
+#' A class to represent clonality metrics
+#'
+#' @slot most_clonotype most frequent clonotype
+#' @slot least_clonotype least frequent clonotype
+#' @slot pielou 1-Pielou index
+#' @slot clonal_prop clonal proportion
+#' @slot abundance relative abundance (in all clonotypes)
+#' @slot abundance_top relative abundance (in top 100 clonotypes)
+#' @slot abundance_rare relative abundance (in rare clonotypes)
+#' @exportClass Clonality
+setClass("Clonality",
+  slots = c(
+    most_clonotype = "data.frame",
+    least_clonotype = "data.frame",
+    pielou = "data.frame",
+    clonal_prop = "data.frame",
+    abundance = "data.frame",
+    abundance_top = "data.frame",
+    abundance_rare = "data.frame"
+  )
+)
+
+#' Class "Motif"
+#'
+#' A class to represent motif data
+#'
+#' @slot aa_spectratype aa spectratype data
+#' @slot aa_max_spectratype aa max spectratype data
+#' @slot aa_motif_count aa motif count data
+#' @exportClass Motif
+setClass("Motif",
+  slots = c(
+    aa_spectratype = "data.frame",
+    aa_max_spectratype = "data.frame",
+    aa_motif_count = "data.frame"
+  )
+)
+
 #' Class "reTCRProj"
 #'
 #' A class to represent a reTCR project
 #'
-#' @slot data contains the main data for the project.
-#' @slot basic contains basic analysis information.
-#' @slot diversity contains diversity analysis information.
+#' @slot data contains the main data for the project
+#' @slot basic contains basic metrics
+#' @slot diversity contains diversity metrics
+#' @slot clonality contains clonality metrics
 #' @exportClass reTCRProj
 setClass("reTCRProj",
   slots = c(
     data = "data.frame",
     basic = "Basic",
-    diversity = "Diversity"
+    diversity = "Diversity",
+    clonality = "Clonality"
   )
 )

R/utils-clonality.R

@@ -0,0 +1,12 @@
+.get_clonality <- function(data, attr_col) {
+  return(methods::new(
+    "Clonality",
+    most_clonotype = data.frame(),
+    least_clonotype = data.frame(),
+    pielou = data.frame(),
+    clonal_prop = data.frame(),
+    abundance = data.frame(),
+    abundance_top = data.frame(),
+    abundance_rare = data.frame()
+  ))
+}

README.md

@@ -89,4 +89,29 @@ print(proj@diversity@chao1)
 
 # Gini coefficient
 print(proj@diversity@gini_coeff)
+```
+
+## 3. Clonality Analysis
+
+``` r
+# most frequent clonotypes
+print(proj@clonality@most_clonotype)
+
+# least frequent clonotypes
+print(proj@clonality@least_clonotype)
+
+# 1-Pielou index
+print(proj@clonality@pielou)
+
+# clonal proportion
+print(proj@clonality@clonal_prop)
+
+# relative abundance (in all clonotypes)
+print(proj@clonality@abundance)
+
+# relative abundance (in top 100 clonotypes)
+print(proj@clonality@abundance_top)
+
+# relative abundance (in rare clonotypes)
+print(proj@clonality@abundance_rare)
 ```