Merge pull request #7 from EmanuelSoda/fix

another quick fix
EmanuelSoda · Sep 5, 2023 · fe36a9c · fe36a9c
2 parents 92e60ce + ccf23dc
commit fe36a9c
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Showing 3 changed files with 30 additions and 17 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ScreenR
 Type: Package
 Title: Package to Perform High Throughput Biological Screening
-Version: 0.99.54
+Version: 0.99.55
 Date: 2023-09-05 
 Authors@R: c(person("Emanuel Michele", "Soda", role = c("aut", "cre"),
                   email = "[email protected]", 

diff --git a/R/filter_by.R b/R/filter_by.R
@@ -29,32 +29,44 @@
 #' )
 #'
 filter_by_slope <- function(screenR_Object, genes, group_var_treatment,
-    group_var_control, slope_control, slope_treatment) {
+    group_var_control, slope_control = NULL, slope_treatment = NULL) {
 
     # Compute the slope of the hits in the treatment Samples
-    slope_treatment <- ScreenR::compute_slope(screenR_Object, genes,
+    slope_trt <- ScreenR::compute_slope(screenR_Object, genes,
         group_var = group_var_treatment
     )
 
 
     # Compute the slope of the hits in the control Samples
-    slope_DMSO <- ScreenR::compute_slope(screenR_Object, genes,
+    slope_contr <- ScreenR::compute_slope(screenR_Object, genes,
         group_var = group_var_control
     )
 
     data <- screenR_Object@data_table
 
-    data <- dplyr::left_join(data, slope_treatment, by = "Gene")
+    data <- dplyr::left_join(data, slope_trt, by = "Gene")
     data <- dplyr::rename(data, slope_treatment = .data$Slope)
 
-    data <- dplyr::left_join(data, slope_DMSO, by = "Gene")
+    data <- dplyr::left_join(data, slope_contr, by = "Gene")
     data <- dplyr::rename(data, slope_control = .data$Slope)
 
-
-    data <- dplyr::filter(data, .data$slope_control >= slope_control)
-
-    data <- dplyr::filter(data, .data$slope_treatment <= slope_treatment)
-
+    if(!is.null(slope_control)){
+        print(unique(data$slope_control))
+        data <- dplyr::filter(data, abs(.data$slope_control)  <=
+                                  abs(slope_control))
+    }
+
+    if(!is.null(slope_treatment)){
+        data <- dplyr::filter(data, abs(.data$slope_treatment) >=
+                                  abs(slope_treatment))
+    }
+
+    # The treatment has more effect than the control 
+    data <- dplyr::filter(data, abs(.data$slope_control) <= 
+                              abs(.data$slope_treatment))
+
+    data <- dplyr::distinct(data, .data$Gene, 
+                            .data$slope_control, .data$slope_treatment)
     return(data)
 }
 

diff --git a/tests/testthat/test-filter.R b/tests/testthat/test-filter.R
@@ -80,15 +80,16 @@ test_that("filter_by_slope_fold", {
     library(tibble)
     object <- create_test_object()
 
-    data <- filter_by_slope(
+    data_p <- filter_by_slope(
         screenR_Object = object,
-        genes = c("Gene_1", "Gene_300"),
+        genes = c("Gene_1", "Gene_2", "Gene_3", "Gene_4", "Gene_5",
+                  "Gene_6", "Gene_7", "Gene_8", "Gene_9", "Gene_10",
+                  "Gene_11", "Gene_12", "Gene_13", "Gene_14", "Gene_15"),
         group_var_treatment = c("T1", "T2", "TRT"),
         group_var_control = c("T1", "T2", "Time3", "Time4"),
-        slope_treatment = -0.5, slope_control = 0.5
-    )
-    expect_equal(class(data)[1], "tbl_df")
-    #data %>%  dplyr::select(-c("Sequence", "Library", "Gene_ID"))
+        slope_treatment = NULL, slope_control = NULL
+    ) 
+    expect_true(all(abs(data_p$slope_treatment) > abs(data_p$slope_control)))
 })