plotting functions work with CIRI2

BIMSBbioinfo · Mar 9, 2017 · 66e6fdd · 66e6fdd
1 parent 125c8ab
commit 66e6fdd
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Showing 2 changed files with 15 additions and 8 deletions.
diff --git a/R/visualize.R b/R/visualize.R
@@ -151,7 +151,14 @@ setMethod("uniqReadsQC",
           signature("RangedSummarizedExperiment"),
           definition=function(se, sample) {
 
-            if (sample != "all" & !(sample %in% colnames(se))) stop(sample, ' is not a valid sample.')
+            # this makes sense only for find_circ analyses,
+            # CIRI does not report unique reads
+            if (!("circ.uniq" %in% names(assays(se)))) {
+              stop('circ.uniq assay does not exist')
+            }
+            if (sample != "all" & !(sample %in% colnames(se))) {
+              stop(sample, ' is not a valid sample.')
+            }
 
             SMPL <- sample
             if (sample == "all") {

diff --git a/inst/scripts/test_load_data.R b/inst/scripts/test_load_data.R
@@ -4,12 +4,12 @@ cdata <- data.frame(sample=c("riboz", "RNaseR"),
                     filename=c("inst/extdata/ciri_demo_hek/HEK_riborezo_CIRI_sites.txt",
                                "inst/extdata/ciri_demo_hek/HEK_RNaseR_CIRI_sites.txt"))
 
-colData <- cdata
-keep.linear <- TRUE
-wobble <- 1
-subs <- "all"
-qualfilter <- FALSE
-keepCols <- 1:12
+# colData <- cdata
+# keep.linear <- TRUE
+# wobble <- 1
+# subs <- "all"
+# qualfilter <- FALSE
+# keepCols <- 1:12
 
 
 circs.se <- summarizeCircs(colData = cdata, keep.linear = FALSE, wobble = 1, subs = "all", qualfilter = FALSE, keepCols = 1:12)
@@ -31,7 +31,7 @@ circs.se <- annotateCircs(se = circs.se, annot.list = annot.list, assembly = "hg
 
 histogram(circs.se, 0.5)
 annotPie(circs.se, 0.02)
-uniqReadsQC(circs.se, "D0")
+uniqReadsQC(circs.se, "all")
 
 # development
 #library(data.table)