From 627d36030029d557cbb9b79af961b67655b5df96 Mon Sep 17 00:00:00 2001 From: Shixiang Wang Date: Wed, 13 Apr 2022 15:29:06 +0800 Subject: [PATCH] update pkg site --- .Rbuildignore | 1 + CRAN-SUBMISSION | 3 + docs/404.html | 4 +- docs/CONTRIBUTING.html | 4 +- docs/LICENSE.html | 4 +- docs/articles/api.html | 8 +- docs/articles/index.html | 4 +- docs/authors.html | 8 +- docs/index.html | 5 +- docs/news/index.html | 10 +- docs/pkgdown.yml | 2 +- docs/reference/TCGA.organ.html | 6 +- docs/reference/UCSCXenaShiny.html | 4 +- .../analyze_gene_drug_response_asso.html | 20 +- .../analyze_gene_drug_response_diff.html | 66 +- docs/reference/app_run.html | 10 +- docs/reference/available_hosts.html | 9 +- docs/reference/ccle_absolute.html | 6 +- docs/reference/ccle_info.html | 6 +- docs/reference/ezcor.html | 4 +- docs/reference/ezcor_batch.html | 4 +- docs/reference/ezcor_partial_cor.html | 4 +- docs/reference/get_pancan_value.html | 28 +- docs/reference/index.html | 4 +- docs/reference/keep_cat_cols.html | 4 +- docs/reference/load_data.html | 17657 +++++++++++++++- docs/reference/pcawg_info.html | 6 +- docs/reference/pcawg_purity.html | 6 +- docs/reference/pipe.html | 4 +- docs/reference/query_molecule_value.html | 31 +- docs/reference/query_pancan_value.html | 50 +- docs/reference/query_toil_value_df.html | 20 +- docs/reference/tcga_clinical.html | 6 +- docs/reference/tcga_genome_instability.html | 6 +- docs/reference/tcga_gtex.html | 6 +- docs/reference/tcga_purity.html | 6 +- docs/reference/tcga_subtypes.html | 6 +- docs/reference/tcga_surv.html | 6 +- docs/reference/tcga_surv_analysis.html | 20 +- docs/reference/tcga_tmb.html | 7 +- docs/reference/toil_info.html | 6 +- docs/reference/vis_ccle_gene_cor.html | 4 +- docs/reference/vis_ccle_tpm.html | 4 +- docs/reference/vis_gene_TIL_cor.html | 10 +- docs/reference/vis_gene_cor.html | 4 +- docs/reference/vis_gene_cor_cancer.html | 4 +- .../vis_gene_drug_response_asso.html | 4 +- .../vis_gene_drug_response_diff.html | 4 +- docs/reference/vis_gene_immune_cor.html | 10 +- docs/reference/vis_gene_msi_cor.html | 10 +- docs/reference/vis_gene_stemness_cor.html | 32 +- docs/reference/vis_gene_tmb_cor.html | 10 +- docs/reference/vis_identifier_cor.html | 42 +- .../vis_identifier_grp_comparison.html | 58 +- docs/reference/vis_identifier_grp_surv.html | 54 +- docs/reference/vis_identifier_multi_cor.html | 14 +- docs/reference/vis_pancan_anatomy.html | 4 +- docs/reference/vis_pcawg_dist.html | 10 +- docs/reference/vis_pcawg_gene_cor.html | 4 +- docs/reference/vis_pcawg_unicox_tree.html | 10 +- docs/reference/vis_toil_TvsN.html | 18 +- docs/reference/vis_toil_TvsN_cancer.html | 4 +- docs/reference/vis_unicox_tree.html | 10 +- 63 files changed, 18040 insertions(+), 355 deletions(-) create mode 100644 CRAN-SUBMISSION diff --git a/.Rbuildignore b/.Rbuildignore index 25842903..84c78b0e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -43,3 +43,4 @@ inst/extdata/transcript_identifier.rda Dockerfile deploy.* .dockerignore +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 00000000..49de9a65 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.1.7 +Date: 2022-04-13 07:27:25 UTC +SHA: 5302482f1e4b780ae6311d9196e40ffe64380afe diff --git a/docs/404.html b/docs/404.html index d702b34d..350ebf2b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -49,7 +49,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -59,7 +59,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -60,7 +60,7 @@ Reference
  • - vignettes/api.Rmd @@ -121,7 +121,7 @@

    2022-01-27

     library(UCSCXenaShiny)
 #> =========================================================================================
-#> UCSCXenaShiny version 1.1.6
+#> UCSCXenaShiny version 1.1.5
 #> Project URL: https://github.com/openbiox/UCSCXenaShiny
 #> Usages: https://openbiox.github.io/UCSCXenaShiny/
 #> 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 5586afbf..4fc41843 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -29,7 +29,7 @@
       
       
         UCSCXenaShiny
-        1.1.6
+        1.1.7
    @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • -

    https://github.com/openbiox/UCSCXenaShiny. +R package version 1.1.7, https://github.com/openbiox/UCSCXenaShiny. 

    @Manual{,
   title = {UCSCXenaShiny: Interactive Analysis of UCSC Xena Data},
   author = {Shixiang Wang and Yi Xiong and Longfei Zhao and Kai Gu and Yin Li and Fei Zhao},
   year = {2022},
-  note = {R package version 1.1.6},
+  note = {R package version 1.1.7},
   url = {https://github.com/openbiox/UCSCXenaShiny},
 }
    diff --git a/docs/index.html b/docs/index.html index 9e4000a8..5d2c4e2f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -53,7 +53,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -63,7 +63,7 @@ Reference
  • -
  • lifecycle
  • Lines Of Code
    • +
  • check in Biotreasury
    • diff --git a/docs/news/index.html b/docs/news/index.html index 45495e6a..cced202e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - NEWS.md +
    +

    UCSCXenaShiny 1.1.7

    +
    • Added option include.Tumor.only to control if include type
      • +
    • Set default theme if flatly not available.
      • +
    • Added example to generate radar plot, close #239
      • +

    UCSCXenaShiny 1.1.6

    • Added description of extra datasets.
      • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 819bb63f..38cedc58 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.2 pkgdown_sha: ~ articles: api: api.html -last_built: 2022-01-27T10:20Z +last_built: 2022-04-13T07:27Z diff --git a/docs/reference/TCGA.organ.html b/docs/reference/TCGA.organ.html index 5830fd3b..8173c638 100644 --- a/docs/reference/TCGA.organ.html +++ b/docs/reference/TCGA.organ.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7
    @@ -38,7 +38,7 @@ Reference
  • - 
    data("TCGA.organ")
+    
    data("TCGA.organ")
    diff --git a/docs/reference/UCSCXenaShiny.html b/docs/reference/UCSCXenaShiny.html index 21aa0278..b97384aa 100644 --- a/docs/reference/UCSCXenaShiny.html +++ b/docs/reference/UCSCXenaShiny.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -39,7 +39,7 @@ Reference
  • - 
    c("TP53", "KRAS"))
-analyze_gene_drug_response_asso(c("TP53", "KRAS"), combine = TRUE)
-
-# Visualization
-vis_gene_drug_response_asso("TP53")
-}
+    
    if (FALSE) {
+analyze_gene_drug_response_asso("TP53")
+analyze_gene_drug_response_asso(c("TP53", "KRAS"))
+analyze_gene_drug_response_asso(c("TP53", "KRAS"), combine = TRUE)
+
+# Visualization
+vis_gene_drug_response_asso("TP53")
+}
    diff --git a/docs/reference/analyze_gene_drug_response_diff.html b/docs/reference/analyze_gene_drug_response_diff.html index 795638e0..d1ad4ebd 100644 --- a/docs/reference/analyze_gene_drug_response_diff.html +++ b/docs/reference/analyze_gene_drug_response_diff.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    c(
-  "prostate", "central_nervous_system", "urinary_tract", "haematopoietic_and_lymphoid_tissue",
-  "kidney", "thyroid", "soft_tissue", "skin", "salivary_gland",
-  "ovary", "lung", "bone", "endometrium", "pancreas", "breast",
-  "large_intestine", "upper_aerodigestive_tract", "autonomic_ganglia",
-  "stomach", "liver", "biliary_tract", "pleura", "oesophagus"
-)
-
-drug_list <- c(
-  "AEW541", "Nilotinib", "17-AAG", "PHA-665752", "Lapatinib",
-  "Nutlin-3", "AZD0530", "PF2341066", "L-685458", "ZD-6474", "Panobinostat",
-  "Sorafenib", "Irinotecan", "Topotecan", "LBW242", "PD-0325901",
-  "PD-0332991", "Paclitaxel", "AZD6244", "PLX4720", "RAF265", "TAE684",
-  "TKI258", "Erlotinib"
-)
-
-target_list <- c(
-  "IGF1R", "ABL", "HSP90", "c-MET", "EGFR", "MDM2", "GS", "HDAC",
-  "RTK", "TOP1", "XIAP", "MEK", "CDK4", "TUBB1", "RAF", "ALK", "FGFR"
-)
-if (FALSE) {
-analyze_gene_drug_response_diff("TP53")
-analyze_gene_drug_response_diff(c("TP53", "KRAS"), drug = "AEW541")
-analyze_gene_drug_response_diff(c("TP53", "KRAS"),
-  tissue = "kidney",
-  combine = TRUE
-)
-
-# Visualization
-vis_gene_drug_response_diff("TP53")
-}
+    
    tissue_list <- c(
+  "prostate", "central_nervous_system", "urinary_tract", "haematopoietic_and_lymphoid_tissue",
+  "kidney", "thyroid", "soft_tissue", "skin", "salivary_gland",
+  "ovary", "lung", "bone", "endometrium", "pancreas", "breast",
+  "large_intestine", "upper_aerodigestive_tract", "autonomic_ganglia",
+  "stomach", "liver", "biliary_tract", "pleura", "oesophagus"
+)
+
+drug_list <- c(
+  "AEW541", "Nilotinib", "17-AAG", "PHA-665752", "Lapatinib",
+  "Nutlin-3", "AZD0530", "PF2341066", "L-685458", "ZD-6474", "Panobinostat",
+  "Sorafenib", "Irinotecan", "Topotecan", "LBW242", "PD-0325901",
+  "PD-0332991", "Paclitaxel", "AZD6244", "PLX4720", "RAF265", "TAE684",
+  "TKI258", "Erlotinib"
+)
+
+target_list <- c(
+  "IGF1R", "ABL", "HSP90", "c-MET", "EGFR", "MDM2", "GS", "HDAC",
+  "RTK", "TOP1", "XIAP", "MEK", "CDK4", "TUBB1", "RAF", "ALK", "FGFR"
+)
+if (FALSE) {
+analyze_gene_drug_response_diff("TP53")
+analyze_gene_drug_response_diff(c("TP53", "KRAS"), drug = "AEW541")
+analyze_gene_drug_response_diff(c("TP53", "KRAS"),
+  tissue = "kidney",
+  combine = TRUE
+)
+
+# Visualization
+vis_gene_drug_response_diff("TP53")
+}
    diff --git a/docs/reference/app_run.html b/docs/reference/app_run.html index 48c21d7f..1cb86f5a 100644 --- a/docs/reference/app_run.html +++ b/docs/reference/app_run.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("ccle_absolute")
+    
    data("ccle_absolute")
    diff --git a/docs/reference/ccle_info.html b/docs/reference/ccle_info.html index f11b3872..c6a733ea 100644 --- a/docs/reference/ccle_info.html +++ b/docs/reference/ccle_info.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("ccle_info")
+    
    data("ccle_info")
    diff --git a/docs/reference/ezcor.html b/docs/reference/ezcor.html index 00485a5c..92bf8f49 100644 --- a/docs/reference/ezcor.html +++ b/docs/reference/ezcor.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -40,7 +40,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("pcawg_info")
+    
    data("pcawg_info")
    diff --git a/docs/reference/pcawg_purity.html b/docs/reference/pcawg_purity.html index a1418572..3ef594fe 100644 --- a/docs/reference/pcawg_purity.html +++ b/docs/reference/pcawg_purity.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("pcawg_purity")
+    
    data("pcawg_purity")
    diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html index a17e5044..65adb3f4 100644 --- a/docs/reference/pipe.html +++ b/docs/reference/pipe.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    table(UCSCXenaTools::XenaData$Type)
-# It is a the UCSC Xena dataset with "Type" equals to "genomicMatrix"
-if (FALSE) {
-dataset <- "ccle/CCLE_copynumber_byGene_2013-12-03"
-x <- query_molecule_value(dataset, "TP53")
-head(x)
-
-signature <- "TP53 + 2*KRAS - 1.3*PTEN" # a space must exist in the string
-y <- query_molecule_value(dataset, signature)
-head(y)
-}
+    
    # What does dense matrix mean?
+table(UCSCXenaTools::XenaData$Type)
+#> 
+#> clinicalMatrix  genomicMatrix genomicSegment mutationVector 
+#>            343            977            152            203 
+# It is a the UCSC Xena dataset with "Type" equals to "genomicMatrix"
+if (FALSE) {
+dataset <- "ccle/CCLE_copynumber_byGene_2013-12-03"
+x <- query_molecule_value(dataset, "TP53")
+head(x)
+
+signature <- "TP53 + 2*KRAS - 1.3*PTEN" # a space must exist in the string
+y <- query_molecule_value(dataset, signature)
+head(y)
+}
    diff --git a/docs/reference/query_pancan_value.html b/docs/reference/query_pancan_value.html index 6a0b01ee..f029b5f5 100644 --- a/docs/reference/query_pancan_value.html +++ b/docs/reference/query_pancan_value.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -39,7 +39,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("tcga_clinical")
+    
    data("tcga_clinical")
    diff --git a/docs/reference/tcga_genome_instability.html b/docs/reference/tcga_genome_instability.html index c8fc4d53..68312a4c 100644 --- a/docs/reference/tcga_genome_instability.html +++ b/docs/reference/tcga_genome_instability.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("tcga_genome_instability")
+    
    data("tcga_genome_instability")
    diff --git a/docs/reference/tcga_gtex.html b/docs/reference/tcga_gtex.html index 507b8d6c..bc6c3b1b 100644 --- a/docs/reference/tcga_gtex.html +++ b/docs/reference/tcga_gtex.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("tcga_gtex")
+    
    data("tcga_gtex")
    diff --git a/docs/reference/tcga_purity.html b/docs/reference/tcga_purity.html index bcc8871d..5b4baf87 100644 --- a/docs/reference/tcga_purity.html +++ b/docs/reference/tcga_purity.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("tcga_purity")
+    
    data("tcga_purity")
    diff --git a/docs/reference/tcga_subtypes.html b/docs/reference/tcga_subtypes.html index 6d1d019d..4e87c8f6 100644 --- a/docs/reference/tcga_subtypes.html +++ b/docs/reference/tcga_subtypes.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("tcga_subtypes")
+    
    data("tcga_subtypes")
    diff --git a/docs/reference/tcga_surv.html b/docs/reference/tcga_surv.html index 7d458b0d..8ee387e9 100644 --- a/docs/reference/tcga_surv.html +++ b/docs/reference/tcga_surv.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("tcga_surv")
+    
    data("tcga_surv")
    diff --git a/docs/reference/tcga_surv_analysis.html b/docs/reference/tcga_surv_analysis.html index ddaae314..99cc1e33 100644 --- a/docs/reference/tcga_surv_analysis.html +++ b/docs/reference/tcga_surv_analysis.html @@ -35,7 +35,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -44,7 +44,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("tcga_tmb")
+    
    data("tcga_tmb")
+#> Warning: data set 'tcga_tmb' not found
    diff --git a/docs/reference/toil_info.html b/docs/reference/toil_info.html index a52a08fe..5d3516e7 100644 --- a/docs/reference/toil_info.html +++ b/docs/reference/toil_info.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    data("toil_info")
+    
    data("toil_info")
    diff --git a/docs/reference/vis_ccle_gene_cor.html b/docs/reference/vis_ccle_gene_cor.html index b7b952b4..b9340295 100644 --- a/docs/reference/vis_ccle_gene_cor.html +++ b/docs/reference/vis_ccle_gene_cor.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    c(
-  "TCGA-D5-5538-01", "TCGA-VM-A8C8-01",
-  "TCGA-ZN-A9VQ-01", "TCGA-EE-A17X-06",
-  "TCGA-05-4420-01"
-)
-vis_identifier_cor(dataset, id1, dataset, id2, samples)
-
-dataset1 <- "TCGA-BLCA.htseq_counts.tsv"
-dataset2 <- "TCGA-BLCA.gistic.tsv"
-id1 <- "TP53"
-id2 <- "KRAS"
-vis_identifier_cor(dataset1, id1, dataset2, id2)
-}
+    
    if (FALSE) {
+dataset <- "TcgaTargetGtex_rsem_isoform_tpm"
+id1 <- "TP53"
+id2 <- "KRAS"
+vis_identifier_cor(dataset, id1, dataset, id2)
+
+samples <- c(
+  "TCGA-D5-5538-01", "TCGA-VM-A8C8-01",
+  "TCGA-ZN-A9VQ-01", "TCGA-EE-A17X-06",
+  "TCGA-05-4420-01"
+)
+vis_identifier_cor(dataset, id1, dataset, id2, samples)
+
+dataset1 <- "TCGA-BLCA.htseq_counts.tsv"
+dataset2 <- "TCGA-BLCA.gistic.tsv"
+id1 <- "TP53"
+id2 <- "KRAS"
+vis_identifier_cor(dataset1, id1, dataset2, id2)
+}
    diff --git a/docs/reference/vis_identifier_grp_comparison.html b/docs/reference/vis_identifier_grp_comparison.html index f53bcbb0..261aae2a 100644 --- a/docs/reference/vis_identifier_grp_comparison.html +++ b/docs/reference/vis_identifier_grp_comparison.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • -

    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(), +(e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.).

    ...

    other parameters passing to ggstatsplot::ggbetweenstats or ggstatsplot::ggwithinstats.

    @@ -154,32 +154,32 @@

    Value

    Examples

    - 
    if (FALSE) {
-library(UCSCXenaTools)
-expr_dataset <- "TCGA.LUAD.sampleMap/HiSeqV2_percentile"
-cli_dataset <- "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
-id <- "TP53"
-cli_df <- XenaGenerate(
-  subset = XenaDatasets == "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
-) %>%
-  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"))
-)
-
-# When not use the value of `identifier` from `dataset`
-vis_identifier_grp_comparison(grp_df = cli_df[, c(1, 2, 71)])
-vis_identifier_grp_comparison(grp_df = cli_df[, c(1, 2, 71, 111)])
-}
-
+    
    if (FALSE) {
+library(UCSCXenaTools)
+expr_dataset <- "TCGA.LUAD.sampleMap/HiSeqV2_percentile"
+cli_dataset <- "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
+id <- "TP53"
+cli_df <- XenaGenerate(
+  subset = XenaDatasets == "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
+) %>%
+  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"))
+)
+
+# When not use the value of `identifier` from `dataset`
+vis_identifier_grp_comparison(grp_df = cli_df[, c(1, 2, 71)])
+vis_identifier_grp_comparison(grp_df = cli_df[, c(1, 2, 71, 111)])
+}
+
    diff --git a/docs/reference/vis_identifier_grp_surv.html b/docs/reference/vis_identifier_grp_surv.html index 30a36850..894aefa3 100644 --- a/docs/reference/vis_identifier_grp_surv.html +++ b/docs/reference/vis_identifier_grp_surv.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    library(UCSCXenaTools)
-expr_dataset <- "TCGA.LUAD.sampleMap/HiSeqV2_percentile"
-cli_dataset <- "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
-id <- "KRAS"
-cli_df <- XenaGenerate(
-  subset = XenaDatasets == "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
-) %>%
-  XenaQuery() %>%
-  XenaDownload() %>%
-  XenaPrepare()
-
-# Use individual survival data
-surv_df1 <- cli_df[, c("sampleID", "ABSOLUTE_Ploidy", "days_to_death", "vital_status")]
-surv_df1$vital_status <- ifelse(surv_df1$vital_status == "DECEASED", 1, 0)
-vis_identifier_grp_surv(surv_df = surv_df1)
-
-# Use both dataset argument and vis_identifier_grp_surv(surv_df = surv_df1)
-surv_df2 <- surv_df1[, c(1, 3, 4)]
-vis_identifier_grp_surv(expr_dataset, id, surv_df = surv_df2)
-vis_identifier_grp_surv(expr_dataset, id,
-  surv_df = surv_df2,
-  cutoff_mode = "Custom", cutpoint = c(25, 75)
-)
-}
+    
    if (FALSE) {
+library(UCSCXenaTools)
+expr_dataset <- "TCGA.LUAD.sampleMap/HiSeqV2_percentile"
+cli_dataset <- "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
+id <- "KRAS"
+cli_df <- XenaGenerate(
+  subset = XenaDatasets == "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
+) %>%
+  XenaQuery() %>%
+  XenaDownload() %>%
+  XenaPrepare()
+
+# Use individual survival data
+surv_df1 <- cli_df[, c("sampleID", "ABSOLUTE_Ploidy", "days_to_death", "vital_status")]
+surv_df1$vital_status <- ifelse(surv_df1$vital_status == "DECEASED", 1, 0)
+vis_identifier_grp_surv(surv_df = surv_df1)
+
+# Use both dataset argument and vis_identifier_grp_surv(surv_df = surv_df1)
+surv_df2 <- surv_df1[, c(1, 3, 4)]
+vis_identifier_grp_surv(expr_dataset, id, surv_df = surv_df2)
+vis_identifier_grp_surv(expr_dataset, id,
+  surv_df = surv_df2,
+  cutoff_mode = "Custom", cutpoint = c(25, 75)
+)
+}
    diff --git a/docs/reference/vis_identifier_multi_cor.html b/docs/reference/vis_identifier_multi_cor.html index f2693f50..bf5907be 100644 --- a/docs/reference/vis_identifier_multi_cor.html +++ b/docs/reference/vis_identifier_multi_cor.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - 
    c("TP53", "KRAS", "PTEN")
-vis_identifier_multi_cor(dataset, ids)
-}
+    
    if (FALSE) {
+dataset <- "TcgaTargetGtex_rsem_isoform_tpm"
+ids <- c("TP53", "KRAS", "PTEN")
+vis_identifier_multi_cor(dataset, ids)
+}
    diff --git a/docs/reference/vis_pancan_anatomy.html b/docs/reference/vis_pancan_anatomy.html index 0bf5d15d..3447c2f3 100644 --- a/docs/reference/vis_pancan_anatomy.html +++ b/docs/reference/vis_pancan_anatomy.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • - c("#DF2020", "#DDDF21"), TCGA.only = FALSE, draw_quantiles = c(0.25, 0.5, 0.75), - trim = TRUE + trim = TRUE, + include.Tumor.only = FALSE ) @@ -124,6 +125,9 @@

    Arguments

    draw quantiles for violinplot

    trim

    whether trim the violin

    +
    include.Tumor.only
    +

    if TRUE, include "UVM" and "MESO" these two types +with matched normals samples.

    Value

    @@ -132,10 +136,10 @@

    Value

    Examples

    - 
    if (FALSE) {
-p <- vis_toil_TvsN(Gene = "TP53", Mode = "Violinplot", Show.P.value = FALSE, Show.P.label = FALSE)
-p <- vis_toil_TvsN(Gene = "TP53", Mode = "Boxplot", Show.P.value = FALSE, Show.P.label = FALSE)
-}
+    
    if (FALSE) {
+p <- vis_toil_TvsN(Gene = "TP53", Mode = "Violinplot", Show.P.value = FALSE, Show.P.label = FALSE)
+p <- vis_toil_TvsN(Gene = "TP53", Mode = "Boxplot", Show.P.value = FALSE, Show.P.label = FALSE)
+}
    diff --git a/docs/reference/vis_toil_TvsN_cancer.html b/docs/reference/vis_toil_TvsN_cancer.html index ddf9dfae..37e8cefd 100644 --- a/docs/reference/vis_toil_TvsN_cancer.html +++ b/docs/reference/vis_toil_TvsN_cancer.html @@ -29,7 +29,7 @@ UCSCXenaShiny - 1.1.6 + 1.1.7
    @@ -38,7 +38,7 @@ Reference
  • - UCSCXenaShiny - 1.1.6 + 1.1.7 @@ -38,7 +38,7 @@ Reference
  • -