diff --git a/DESCRIPTION b/DESCRIPTION index 710954c..5104aa0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: rPHG -Version: 0.2.1 +Version: 0.2.2 Date: 2019-06-03 Title: R front-end for the practical haplotype graph Authors@R: c( @@ -72,6 +72,6 @@ Encoding: UTF-8 LazyData: true VignetteBuilder: knitr -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 biocViews: GenomeWideAssociation diff --git a/NEWS b/NEWS index 77d13af..3f967b6 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,8 @@ +## CHANGES IN VERSION 0.2.2 +* Fixed issue with `DEMO` method endpoint returning incorrect dimensional data + for specific Maize PHGv1 methods + + ## CHANGES IN VERSION 0.2.1 * Added new function, `plotDot()` + Creates dot plots from `.anchorspro` files diff --git a/NEWS.md b/NEWS.md index e8bf1b3..eaa6f11 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +## rPHG 0.2.2 +* Fixed issue with `DEMO` method endpoint returning incorrect dimensional data + for specific Maize PHGv1 methods + + ## rPHG 0.2.1 * Added new function, `plotDot()` + Creates dot plots from `.anchorspro` files diff --git a/R/class_phg_method.R b/R/class_phg_method.R index 6944fe3..6387135 100644 --- a/R/class_phg_method.R +++ b/R/class_phg_method.R @@ -251,7 +251,7 @@ setMethod( if (conType == "local") { phgDataSetFromLocal(conObj, conMethod, verbose) } else if (conType == "server") { - phgDataSetFromServer(conObj, conMethod, verbose, conDemo) + phgDataSetFromServer(conObj, conMethod, conDemo, verbose) } } ) diff --git a/R/constants.R b/R/constants.R index 2a1eac4..986a6f7 100644 --- a/R/constants.R +++ b/R/constants.R @@ -25,7 +25,7 @@ BRAPI_PARAMS <- list( "METHOD_RR_SIZE" = "dimensionCallSetPageSize=%i", "METHOD_RR_PAGE" = "dimensionCallSetPage=%i", "METHOD_SAMPLE_SIZE" = "dimensionVariantPageSize=%i", - "METHOD_SAMPLE_PAGE" = "dimensionVariantPagePage=%i" + "METHOD_SAMPLE_PAGE" = "dimensionVariantPage=%i" ) diff --git a/R/read_hap_ids.R b/R/read_hap_ids.R index c1b5162..836991a 100644 --- a/R/read_hap_ids.R +++ b/R/read_hap_ids.R @@ -73,6 +73,7 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) { ) ) + message(verbInfo[2]) pb <- utils::txtProgressBar( min = 0, @@ -92,7 +93,7 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) { message(verbInfo[3]) fullResp <- do.call( - what = "cbind", + what = "rbind", args = lapply( X = respVector, FUN = function(x) { @@ -101,10 +102,10 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) { ) ) - colnames(fullResp) <- paste0("R", seq_len(ncol(fullResp))) - rownames(fullResp) <- samplesFromServer(conObj, conMethod, conDemo) + rownames(fullResp) <- paste0("R", seq_len(nrow(fullResp))) + colnames(fullResp) <- samplesFromServer(conObj, conMethod, conDemo) - return(fullResp) + return(t(fullResp)) } diff --git a/R/read_ref_ranges.R b/R/read_ref_ranges.R index b3bc74e..e9ce144 100644 --- a/R/read_ref_ranges.R +++ b/R/read_ref_ranges.R @@ -29,7 +29,7 @@ refRangesFromServer <- function(conObj, conMethod, conDemo) { if (conDemo) { BRAPI_PARAMS$DEMO_N_RR_TOTAL } else { - BRAPI_PARAMS$MAX_N_RR_SIZE + BRAPI_PARAMS$MAX_N_RR_TOTAL } ) ) diff --git a/R/utilities_api_brapi.R b/R/utilities_api_brapi.R index a643ae9..ea6ace4 100644 --- a/R/utilities_api_brapi.R +++ b/R/utilities_api_brapi.R @@ -36,7 +36,7 @@ amUrlContextStringBuilder <- function( BRAPI_PARAMS$REST_KV_SEP, BRAPI_PARAMS$METHOD_SAMPLE_PAGE ), - methodId, rrPageSize, samplePageSize, rrPage, samplePage + methodId, rrPageSize, samplePageSize, samplePage, rrPage ) return(amContextString) diff --git a/vignettes/rphg_walkthrough.Rmd b/vignettes/rphg_walkthrough.Rmd index 2c64d49..371fb4e 100644 --- a/vignettes/rphg_walkthrough.Rmd +++ b/vignettes/rphg_walkthrough.Rmd @@ -85,7 +85,7 @@ If you would like to use a PHG web service, we can use the following similar method: ```{r, echo=TRUE, eval=TRUE} -"demo.hub.maizegenetics.net" |> PHGServerCon() +"phg.maizegdb.org" |> PHGServerCon() ``` Here, a URL pointing to a PHG web service is supplied to the