diff --git a/DESCRIPTION b/DESCRIPTION index 4ba7aa36..5b44ac3a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -80,4 +80,4 @@ VignetteBuilder: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.1.9001 +RoxygenNote: 7.1.2 diff --git a/NAMESPACE b/NAMESPACE index 5d7022b7..60a9357e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -65,6 +65,7 @@ importFrom(psych,corr.test) importFrom(shiny,shinyAppFile) importFrom(stats,complete.cases) importFrom(stats,median) +importFrom(stats,na.omit) importFrom(stats,prcomp) importFrom(stats,predict) importFrom(stats,quantile) diff --git a/NEWS.md b/NEWS.md index 4e890230..068b95c5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # UCSCXenaShiny 1.1.2 +- Fixed value query for gene signature with `purrr` lambda function. - Updated dataset doc. - Uploaded zenodo link. - Uploaded this tool to conda forge, the user can install it from conda now. diff --git a/R/query_value.R b/R/query_value.R index 513fd8db..10c60811 100644 --- a/R/query_value.R +++ b/R/query_value.R @@ -107,10 +107,9 @@ query_pancan_value <- function(molecule, message("IDs include ", paste(ids, collapse = ", ")) tryCatch( { - values <- lapply(ids, function(x) { + values <- purrr::map(ids, function(x) { query_value(x, data_type, database, ...) }) - #values <- purrr::map(ids, ~ query_value(., data_type, database, ...)) unit <- if (is.list(values[[1]]) && length(values[[1]]) > 1) values[[1]][[2]] else NULL if (is.null(unit)) { df <- as.data.frame(values %>% purrr::set_names(ids)) diff --git a/R/xenashiny.R b/R/xenashiny.R index ac9af78f..d18c0b86 100644 --- a/R/xenashiny.R +++ b/R/xenashiny.R @@ -5,5 +5,5 @@ #' @import ggplot2 #' @importFrom psych corr.test #' @importFrom utils download.file head install.packages tail -#' @importFrom stats prcomp predict quantile +#' @importFrom stats prcomp predict quantile na.omit NULL diff --git a/docs/articles/api.html b/docs/articles/api.html index 1676b68b..1a886d09 100644 --- a/docs/articles/api.html +++ b/docs/articles/api.html @@ -106,13 +106,13 @@ -
+

Examples of Accessible Functions

Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao

-

2021-10-05

+

2021-11-17

Source: vignettes/api.Rmd @@ -148,7 +148,7 @@

#> "fusion", "promoter", "APOBEC"), database = c("toil", "ccle", #> "pcawg"), reset_id = NULL, ...) #> NULL

-

For TCGA gene expression data, we use Xena dataset with ID TcgaTargetGtex_rsem_gene_tpm which includes 19131 samples with tumor tissue samples and normal tissue samples. The expression value unit is log2(tpm+0.001).

+

For TCGA gene expression data, we use Xena dataset with ID TcgaTargetGtex_rsem_gene_tpm which includes 19131 samples with tumor tissue samples and normal tissue samples. The expression value unit is log2(tpm+0.001).

Let’s check several examples.

diff --git a/docs/articles/api_files/header-attrs-2.11/header-attrs.js b/docs/articles/api_files/header-attrs-2.11/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/articles/api_files/header-attrs-2.11/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/news/index.html b/docs/news/index.html index 49fbe8b8..0a14b180 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -172,6 +172,7 @@

UCSCXenaShiny 1.1.2 Unreleased

    +
  • Fixed value query for gene signature with purrr lambda function.
  • Updated dataset doc.
  • Uploaded zenodo link.
  • Uploaded this tool to conda forge, the user can install it from conda now. For more details, please read the README file.
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 711ee980..5e508a65 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 1.6.1 pkgdown_sha: ~ articles: api: api.html -last_built: 2021-10-05T03:28Z +last_built: 2021-11-17T02:53Z diff --git a/docs/reference/analyze_gene_drug_response_diff.html b/docs/reference/analyze_gene_drug_response_diff.html index a71d8d71..40f34117 100644 --- a/docs/reference/analyze_gene_drug_response_diff.html +++ b/docs/reference/analyze_gene_drug_response_diff.html @@ -203,7 +203,7 @@

    Arg cutpoint -

    cut point (in percent) for High and Low group, default is c(50, 50).

    +

    cut point (in percent) for High and Low group, default is c(50, 50).

    diff --git a/docs/reference/app_run.html b/docs/reference/app_run.html index 2fea04c9..69b9ff9f 100644 --- a/docs/reference/app_run.html +++ b/docs/reference/app_run.html @@ -186,8 +186,11 @@

    Arg port

    The TCP port that the application should listen on. If the port is not specified, and the shiny.port option is set (with -options(shiny.port = XX)), then that port will be used. Otherwise, -use a random port.

    +options(shiny.port = XX)), then that port will be used. Otherwise, +use a random port between 3000:8000, excluding ports that are blocked +by Google Chrome for being considered unsafe: 3659, 4045, 5060, +5061, 6000, 6566, 6665:6669 and 6697. Up to twenty random +ports will be tried.

    diff --git a/docs/reference/ezcor.html b/docs/reference/ezcor.html index bb187c83..3be0c055 100644 --- a/docs/reference/ezcor.html +++ b/docs/reference/ezcor.html @@ -223,7 +223,7 @@

    Arg sig_label -

    whether add symbal of significance. P < 0.001,***; P < 0.01,**; P < 0.05,*; P >=0.05,""

    +

    whether add symbal of significance. P < 0.001,***; P < 0.01,**; P < 0.05,*; P >=0.05,""

    verbose diff --git a/docs/reference/ezcor_batch.html b/docs/reference/ezcor_batch.html index 08b48022..976f2046 100644 --- a/docs/reference/ezcor_batch.html +++ b/docs/reference/ezcor_batch.html @@ -224,7 +224,7 @@

    Arg sig_label -

    whether add symbal of significance. P < 0.001,***; P < 0.01,**; P < 0.05,*; P >=0.05,""

    +

    whether add symbal of significance. P < 0.001,***; P < 0.01,**; P < 0.05,*; P >=0.05,""

    parallel diff --git a/docs/reference/get_pancan_value.html b/docs/reference/get_pancan_value.html index 5f546418..a0ed3bce 100644 --- a/docs/reference/get_pancan_value.html +++ b/docs/reference/get_pancan_value.html @@ -231,12 +231,12 @@

    Arg subtype

    a length-1 chracter representing a regular expression for matching -DataSubtype column of UCSCXenaTools::XenaData.

    +DataSubtype column of UCSCXenaTools::XenaData.

    dataset

    a length-1 chracter representing a regular expression for matching -XenaDatasets of UCSCXenaTools::XenaData.

    +XenaDatasets of UCSCXenaTools::XenaData.

    host diff --git a/docs/reference/load_data.html b/docs/reference/load_data.html index 54d0a6dc..462c4145 100644 --- a/docs/reference/load_data.html +++ b/docs/reference/load_data.html @@ -174,7 +174,7 @@

    Load Dataset Provided by This Package

    Load data from builtin or Zenodo. Option xena.zenodoDir can be used to set default path for storing -extra data from Zenodo, e.g., options(xena.zenodoDir = "/home/xxx/dataset").

    +extra data from Zenodo, e.g., options(xena.zenodoDir = "/home/xxx/dataset").

    load_data(name)
    diff --git a/docs/reference/query_molecule_value.html b/docs/reference/query_molecule_value.html index acfd061d..4369142f 100644 --- a/docs/reference/query_molecule_value.html +++ b/docs/reference/query_molecule_value.html @@ -201,7 +201,7 @@

    Value

    Examples

    # What does dense matrix mean?
-table(UCSCXenaTools::XenaData$Type)
+table(UCSCXenaTools::XenaData$Type)
 # It is a the UCSC Xena dataset with "Type" equals to "genomicMatrix"
 if (FALSE) {
 dataset <- "ccle/CCLE_copynumber_byGene_2013-12-03"
diff --git a/docs/reference/tcga_surv_analysis.html b/docs/reference/tcga_surv_analysis.html
index bbcbe5be..851d6420 100644
--- a/docs/reference/tcga_surv_analysis.html
+++ b/docs/reference/tcga_surv_analysis.html
@@ -245,11 +245,11 @@ 
    Arg
     
     
       cutpoint
-      
    cut point (in percent) for "Custom" mode, default is c(50, 50).
    
+      
    cut point (in percent) for "Custom" mode, default is c(50, 50).
    
     
     
       cnv_type
-      
    only used when profile is "cnv", can select from c("Duplicated", "Normal", "Deleted").
    
+      
    only used when profile is "cnv", can select from c("Duplicated", "Normal", "Deleted").
    
     
     
       palette
diff --git a/docs/reference/vis_gene_drug_response_diff.html b/docs/reference/vis_gene_drug_response_diff.html
index 2b62025f..9a116a38 100644
--- a/docs/reference/vis_gene_drug_response_diff.html
+++ b/docs/reference/vis_gene_drug_response_diff.html
@@ -196,7 +196,7 @@ 
    Arg
     
     
       Show.P.label
-      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
+      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
     
     
       Method
diff --git a/docs/reference/vis_identifier_grp_comparison.html b/docs/reference/vis_identifier_grp_comparison.html
index 424aa7cb..8f7e7815 100644
--- a/docs/reference/vis_identifier_grp_comparison.html
+++ b/docs/reference/vis_identifier_grp_comparison.html
@@ -237,7 +237,7 @@ 
    Arg
 significant comparisons will be shown by default. To change this
 behavior, select appropriate option with pairwise.display argument. The
 pairwise comparison dataframes are prepared using the
-pairwiseComparisons::pairwise_comparisons function. For more details
+pairwise_comparisons function. For more details
 about pairwise comparisons, see the documentation for that function.
    
     
     
@@ -248,9 +248,9 @@ 
    Arg
     
     
       ggtheme
-      
    A ggplot2 theme. Default value is
-ggstatsplot::theme_ggstatsplot(). Any of the ggplot2 themes (e.g.,
-ggplot2::theme_bw()), or themes from extension packages are allowed
+      
    A {ggplot2} theme. Default value is
+ggstatsplot::theme_ggstatsplot(). Any of the {ggplot2} themes (e.g.,
+theme_bw()), or themes from extension packages are allowed
 (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(),
 etc.).
    
     
@@ -270,20 +270,20 @@ 
    Examp
 expr_dataset <- "TCGA.LUAD.sampleMap/HiSeqV2_percentile"
 cli_dataset <- "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
 id <- "TP53"
-cli_df <- XenaGenerate(
+cli_df <- XenaGenerate(
   subset = XenaDatasets == "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
-) %>%
-  XenaQuery() %>%
-  XenaDownload() %>%
-  XenaPrepare()
+) %>%
+  XenaQuery() %>%
+  XenaDownload() %>%
+  XenaPrepare()
 
 # group data.frame with 2 columns
 vis_identifier_grp_comparison(expr_dataset, id, cli_df[, c("sampleID", "gender")])
 # group data.frame with 3 columns
 vis_identifier_grp_comparison(
   expr_dataset, id,
-  cli_df[, c("sampleID", "pathologic_M", "gender")] %>%
-    dplyr::filter(pathologic_M %in% c("M0", "MX"))
+  cli_df[, c("sampleID", "pathologic_M", "gender")] %>%
+    dplyr::filter(pathologic_M %in% c("M0", "MX"))
 )
 
 # When not use the value of `identifier` from `dataset`
diff --git a/docs/reference/vis_identifier_grp_surv.html b/docs/reference/vis_identifier_grp_surv.html
index e2feea44..c8af0308 100644
--- a/docs/reference/vis_identifier_grp_surv.html
+++ b/docs/reference/vis_identifier_grp_surv.html
@@ -212,7 +212,7 @@ 
    Arg
     
     
       cutpoint
-      
    cut point (in percent) for "Custom" mode, default is c(50, 50).
    
+      
    cut point (in percent) for "Custom" mode, default is c(50, 50).
    
     
     
       palette
@@ -235,12 +235,12 @@ 
    Examp
 expr_dataset <- "TCGA.LUAD.sampleMap/HiSeqV2_percentile"
 cli_dataset <- "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
 id <- "KRAS"
-cli_df <- XenaGenerate(
+cli_df <- XenaGenerate(
   subset = XenaDatasets == "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
-) %>%
-  XenaQuery() %>%
-  XenaDownload() %>%
-  XenaPrepare()
+) %>%
+  XenaQuery() %>%
+  XenaDownload() %>%
+  XenaPrepare()
 
 # Use individual survival data
 surv_df1 <- cli_df[, c("sampleID", "ABSOLUTE_Ploidy", "days_to_death", "vital_status")]
diff --git a/docs/reference/vis_pcawg_dist.html b/docs/reference/vis_pcawg_dist.html
index e82422c2..d0cad8f7 100644
--- a/docs/reference/vis_pcawg_dist.html
+++ b/docs/reference/vis_pcawg_dist.html
@@ -209,7 +209,7 @@ 
    Arg
     
     
       Show.P.label
-      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
+      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
     
     
       Method
diff --git a/docs/reference/vis_toil_TvsN.html b/docs/reference/vis_toil_TvsN.html
index 6e12e930..fdd54e4d 100644
--- a/docs/reference/vis_toil_TvsN.html
+++ b/docs/reference/vis_toil_TvsN.html
@@ -210,7 +210,7 @@ 
    Arg
     
     
       Show.P.label
-      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
+      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
     
     
       Method
diff --git a/docs/reference/vis_toil_TvsN_cancer.html b/docs/reference/vis_toil_TvsN_cancer.html
index a17848a4..3da4bd3d 100644
--- a/docs/reference/vis_toil_TvsN_cancer.html
+++ b/docs/reference/vis_toil_TvsN_cancer.html
@@ -209,7 +209,7 @@ 
    Arg
     
     
       Show.P.label
-      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
+      
    TRUE or FALSE present p value with number or label *, **, *** and ****
    
     
     
       Method
diff --git a/man/app_run.Rd b/man/app_run.Rd
index 155165bf..2f4fdbb0 100644
--- a/man/app_run.Rd
+++ b/man/app_run.Rd
@@ -12,7 +12,10 @@ app_run(runMode = "client", port = getOption("shiny.port"))
 \item{port}{The TCP port that the application should listen on. If the
 \code{port} is not specified, and the \code{shiny.port} option is set (with
 \code{options(shiny.port = XX)}), then that port will be used. Otherwise,
-use a random port.}
+use a random port between 3000:8000, excluding ports that are blocked
+by Google Chrome for being considered unsafe: 3659, 4045, 5060,
+5061, 6000, 6566, 6665:6669 and 6697. Up to twenty random
+ports will be tried.}
 }
 \description{
 Run UCSC Xena Shiny App
diff --git a/man/vis_identifier_grp_comparison.Rd b/man/vis_identifier_grp_comparison.Rd
index 9e11439a..78a704b5 100644
--- a/man/vis_identifier_grp_comparison.Rd
+++ b/man/vis_identifier_grp_comparison.Rd
@@ -54,16 +54,16 @@ are to be displayed (default: \code{TRUE}). Please note that only
 \strong{significant} comparisons will be shown by default. To change this
 behavior, select appropriate option with \code{pairwise.display} argument. The
 pairwise comparison dataframes are prepared using the
-\code{pairwiseComparisons::pairwise_comparisons} function. For more details
+\code{pairwise_comparisons} function. For more details
 about pairwise comparisons, see the documentation for that function.}
 
 \item{p.adjust.method}{Adjustment method for \emph{p}-values for multiple
 comparisons. Possible methods are: \code{"holm"} (default), \code{"hochberg"},
 \code{"hommel"}, \code{"bonferroni"}, \code{"BH"}, \code{"BY"}, \code{"fdr"}, \code{"none"}.}
 
-\item{ggtheme}{A \code{ggplot2} theme. Default value is
-\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{ggplot2} themes (e.g.,
-\code{ggplot2::theme_bw()}), or themes from extension packages are allowed
+\item{ggtheme}{A \code{{ggplot2}} theme. Default value is
+\code{ggstatsplot::theme_ggstatsplot()}. Any of the \code{{ggplot2}} themes (e.g.,
+\code{theme_bw()}), or themes from extension packages are allowed
 (e.g., \code{ggthemes::theme_fivethirtyeight()}, \code{hrbrthemes::theme_ipsum_ps()},
 etc.).}