Auto-reformatted some files with Air

Author: lcolladotor

app.R

@@ -18,31 +18,31 @@ options("golem.app.prod" = TRUE)
 ## In this case, I'm using my local files instead of downloading them
 ## by telling fetch_data(destdir) where my local files are stored at.
 if (!exists('spe'))
-  spe <-
-    fetch_data('spe', here::here('data-raw/spatialLIBD_files'))
+    spe <-
+        fetch_data('spe', here::here('data-raw/spatialLIBD_files'))
 if (!exists('sce_layer'))
-  sce_layer <-
-    fetch_data('sce_layer', here::here('data-raw/spatialLIBD_files'))
+    sce_layer <-
+        fetch_data('sce_layer', here::here('data-raw/spatialLIBD_files'))
 if (!exists('modeling_results'))
-  modeling_results <-
-    fetch_data('modeling_results', here::here('data-raw/spatialLIBD_files'))
+    modeling_results <-
+        fetch_data('modeling_results', here::here('data-raw/spatialLIBD_files'))
 
 modeling_results <- lapply(modeling_results, function(x) {
-  colnames(x) <- gsub("ayer", "", colnames(x))
-  return(x)
+    colnames(x) <- gsub("ayer", "", colnames(x))
+    return(x)
 })
 
 sig_genes <-
-  sig_genes_extract_all(
-    n = nrow(sce_layer),
-    modeling_results,
-    sce_layer = sce_layer
-  )
+    sig_genes_extract_all(
+        n = nrow(sce_layer),
+        modeling_results,
+        sce_layer = sce_layer
+    )
 
 options(repos = BiocManager::repositories())
 spatialLIBD::run_app(
-  spe = spe,
-  sce_layer = sce_layer,
-  modeling_results = modeling_results,
-  sig_genes = sig_genes,
+    spe = spe,
+    sce_layer = sce_layer,
+    modeling_results = modeling_results,
+    sig_genes = sig_genes,
 ) # add parameters here (if any)

tests/testthat/test-vis_gene.R

@@ -1,70 +1,67 @@
-test_that(
-    "vis_gene",
-    {
-        if (!exists("spe")) spe <- fetch_data("spe")
+test_that("vis_gene", {
+    if (!exists("spe")) spe <- fetch_data("spe")
 
-        #   Non-numeric column to plot
-        expect_error(
-            {
-                p <- vis_gene(
-                    spe,
-                    geneid = c("sum_umi", rownames(spe)[1], "layer_guess")
-                )
-            },
-            "'geneid' can not contain non-numeric colData columns\\."
-        )
+    #   Non-numeric column to plot
+    expect_error(
+        {
+            p <- vis_gene(
+                spe,
+                geneid = c("sum_umi", rownames(spe)[1], "layer_guess")
+            )
+        },
+        "'geneid' can not contain non-numeric colData columns\\."
+    )
 
-        #   Bad sample ID
-        expect_error(
-            {
-                p <- vis_gene(
-                    spe,
-                    geneid = c("sum_umi", rownames(spe)[1]),
-                    sampleid = "aaa"
-                )
-            },
-            "'spe\\$sample_id' must exist and contain the ID aaa"
-        )
+    #   Bad sample ID
+    expect_error(
+        {
+            p <- vis_gene(
+                spe,
+                geneid = c("sum_umi", rownames(spe)[1]),
+                sampleid = "aaa"
+            )
+        },
+        "'spe\\$sample_id' must exist and contain the ID aaa"
+    )
 
-        #   Bad assayname
-        expect_error(
-            {
-                p <- vis_gene(
-                    spe,
-                    geneid = c("sum_umi", rownames(spe)[1]),
-                    assayname = "aaa"
-                )
-            },
-            "'aaa' is not an assay in 'spe'"
-        )
+    #   Bad assayname
+    expect_error(
+        {
+            p <- vis_gene(
+                spe,
+                geneid = c("sum_umi", rownames(spe)[1]),
+                assayname = "aaa"
+            )
+        },
+        "'aaa' is not an assay in 'spe'"
+    )
 
-        #   Bad geneid
-        expect_error(
-            {
-                p <- vis_gene(spe, geneid = "aaa")
-            },
-            "Could not find the 'geneid'\\(s\\) aaa"
-        )
+    #   Bad geneid
+    expect_error(
+        {
+            p <- vis_gene(spe, geneid = "aaa")
+        },
+        "Could not find the 'geneid'\\(s\\) aaa"
+    )
 
-        #   Trivially check success with legitimate input
-        expect_true(
-            all(
-                c("gg", "ggplot") %in% class(
+    #   Trivially check success with legitimate input
+    expect_true(
+        all(
+            c("gg", "ggplot") %in%
+                class(
                     vis_gene(spe, geneid = c("sum_umi", rownames(spe)[1]))
                 )
-            )
         )
+    )
 
-
-        #   Bad spatialCoords
-        spe_temp <- spe
-        colnames(spatialCoords(spe_temp)) <- c("a", "b")
-        expect_error(
-            {
-                p <- vis_gene(spe_temp, geneid = "sum_umi")
-            },
-            "^Abnormal spatial coordinates"
-        )
-        rm(spe_temp)
-    }
-)
+    #   Bad spatialCoords
+    spe_temp <- spe
+    colnames(spatialCoords(spe_temp)) <- c("a", "b")
+    expect_error(
+        {
+            p <- vis_gene(spe_temp, geneid = "sum_umi")
+        },
+        "^Abnormal spatial coordinates"
+    )
+    rm(spe_temp)
+})