From 42e537461a59b0f83f717ed03b1324e99806dc10 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 22 Dec 2023 13:49:42 +0100 Subject: [PATCH 1/7] Improving README --- README.Rmd | 3 +++ README.md | 5 +++-- inst/sticker/scigenex_logo.png | Bin 0 -> 67006 bytes 3 files changed, 6 insertions(+), 2 deletions(-) create mode 100644 inst/sticker/scigenex_logo.png diff --git a/README.Rmd b/README.Rmd index 3091068..e959865 100644 --- a/README.Rmd +++ b/README.Rmd @@ -11,6 +11,9 @@ html_preview: false library("badger") ``` + + + ```{r, echo = FALSE, results='asis'} cat( badge_lifecycle(stage = "stable", color="green"), diff --git a/README.md b/README.md index 55c32bb..1bc99f7 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,6 @@ - + + + [![](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![Project Status: Active - The project has reached a stable, usable @@ -7,7 +9,6 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re [![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://cran.r-project.org/web/licenses/MIT) [![](https://img.shields.io/github/last-commit/dputhier/scigenex.svg)](https://github.com/dputhier/scigenex/commits/main) -[![Codecov test coverage](https://codecov.io/gh/dputhier/scigenex/branch/main/graph/badge.svg)](https://app.codecov.io/gh/dputhier/scigenex?branch=main) # SciGeneX repository diff --git a/inst/sticker/scigenex_logo.png b/inst/sticker/scigenex_logo.png new file mode 100644 index 0000000000000000000000000000000000000000..19ef5936f61e3d2156f31d6530a99f0397c36ad2 GIT binary patch literal 67006 zcmeFYWmFtp)Fs@wyEX2C;2zuw65QPh1b26L3GNyocyM9 zT1_{Ls;;{C*xvh`icpl7L_s7#1c5*((o*8eAP^)h@X~|_euMDam}r1ESmQ5};=nub z^C;Hl2fQKJOKCZQKunbHF9`P^LarbX8Aw`OMAbd(WX;VTd%r>G;+(Ipqx>FHR8=X4 zZxC!f6kFd&1I_z0~IwsH*_0Ie?Ob>`Zky&$jdJ(g`D?(&=!LZYlxU9YWEV8 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zIQC$mQ+&-6z{dKxkw*0kj~exY*kOTKCN7@>QJAz8o-L0)443)c?s4_qp#e`d%t@$I zbyC{mD*&HEm{`1R94D03OKo0q`qL|Bql;n9cMUB=) w{cj~1|E*-X@nE&O`EwFwp?tgn2~Xb>^@2#Wn?V4w5D55FkX4qclrjnZKS6aQZU6uP literal 0 HcmV?d00001 From d8a847f231d2cb6300f0366a493029f23ea952b9 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 22 Dec 2023 13:53:09 +0100 Subject: [PATCH 2/7] Changed sticker link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1bc99f7..9cdc5c4 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ - + [![](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![Project Status: Active - The project has reached a stable, usable From 16211f407b39111c144ffd4cbdc7913073c0c70e Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 22 Dec 2023 13:54:03 +0100 Subject: [PATCH 3/7] Changed sticker size --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9cdc5c4..ec828a2 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ - + [![](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![Project Status: Active - The project has reached a stable, usable From cf7761af75ba780c1e0f26f89b4802ecedb79213 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 22 Dec 2023 14:39:39 +0100 Subject: [PATCH 4/7] Changed codecov.yml --- codecov.yml | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/codecov.yml b/codecov.yml index 04c5585..d68cda4 100644 --- a/codecov.yml +++ b/codecov.yml @@ -1,14 +1,11 @@ comment: false -coverage: - status: - project: - default: - target: auto - threshold: 1% - informational: true - patch: - default: - target: auto - threshold: 1% - informational: true +language: R + +sudo: false + +cache: packages + +after_success: + +- Rscript -e 'covr::codecov()' From 2b57419a133d5e7feb7cabc736cc83b9f83f0c5f Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 22 Dec 2023 14:39:55 +0100 Subject: [PATCH 5/7] Fix a test --- tests/testthat/test.gene_clustering.R | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/tests/testthat/test.gene_clustering.R b/tests/testthat/test.gene_clustering.R index 6a2ed77..71a200f 100644 --- a/tests/testthat/test.gene_clustering.R +++ b/tests/testthat/test.gene_clustering.R @@ -9,8 +9,7 @@ pbmc3k_medium_clust <- select_genes(data = pbmc3k_medium, test_that("Checking output slots generated by gene_clustering() using keep_nn as FALSE", { # Create output directory tmp_dir <- tempdir() - dir.create() - dir.create("tmp_dir") + dir.create(tmp_dir) ## A rather stringent version res_no_keep_nn <- gene_clustering(object = pbmc3k_medium_clust, @@ -18,7 +17,7 @@ test_that("Checking output slots generated by gene_clustering() using keep_nn as keep_nn = FALSE, s = 5, threads = 6, - output_path = "tmp_dir") + output_path = tmp_dir) # ======================================================= # Test name of temporary files @@ -189,7 +188,7 @@ test_that("Checking output slots generated by gene_clustering() using keep_nn as "inflation" )) - expect_equal(res_no_keep_nn@parameters$output_path, "tmp_dir") + expect_equal(res_no_keep_nn@parameters$output_path, tmp_dir) expect_true(is.character(res_no_keep_nn@parameters$output_path)) expect_equal(length(res_no_keep_nn@parameters$output_path), 1) @@ -246,7 +245,7 @@ test_that("Checking output slots generated by gene_clustering() using keep_nn as expect_true(is.numeric(res_no_keep_nn@gene_clusters_metadata$cluster_id)) # Remove temporary files - unlink("tmp_dir", recursive = TRUE) + unlink(tmp_dir, recursive = TRUE) }) From 1ac075920f15dabd237286bb44539eff8bf6ca50 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 22 Dec 2023 15:55:53 +0100 Subject: [PATCH 6/7] Fixe an issue with temp dir --- R/gene_clustering.R | 41 ++++++++++++++++++++------- man/construct_new_graph.Rd | 2 +- man/gene_clustering.Rd | 2 +- man/keep_dbf_graph.Rd | 2 +- tests/testthat/test.dist2border.R | 3 ++ tests/testthat/test.gene_clustering.R | 2 +- 6 files changed, 37 insertions(+), 15 deletions(-) diff --git a/R/gene_clustering.R b/R/gene_clustering.R index c6a76c4..aab252a 100644 --- a/R/gene_clustering.R +++ b/R/gene_clustering.R @@ -64,10 +64,20 @@ gene_clustering <- function(object = NULL, inflation = 2, method=c("closest_neighborhood", "reciprocal_neighborhood"), threads = 1, - output_path = tempdir(), + output_path = NULL, name = NULL, keep_nn = FALSE) { + if(is.null(output_path)){ + output_path <- tempdir() + dir.create(output_path, recursive = TRUE, showWarnings = FALSE) + }else{ + if (!dir.exists(output_path)) { + dir.create(output_path, recursive = TRUE, showWarnings = FALSE) + } + } + + method <- match.arg(method) @@ -179,19 +189,24 @@ gene_clustering <- function(object = NULL, #' @export construct_new_graph construct_new_graph <- function(object = NULL, k = 5, - output_path = tempdir(), + output_path = NULL, name = NULL) { + + if(is.null(output_path)){ + output_path <- tempdir() + dir.create(output_path, recursive = TRUE, showWarnings = FALSE) + } + ## Check format object arg check_format_cluster_set(object) - ## Generate output path # Get working directory if output_path is "." if (output_path == ".") { output_path <- getwd() } - # Check if output directory exists. If not stop the command. - if (!file.exists(output_path)) { - stop("Output directory provided does not exist.") + + if (!dir.exists(output_path)) { + dir.create(output_path, recursive = TRUE, showWarnings = FALSE) } # Create a random string if name is not provided @@ -376,17 +391,21 @@ construct_new_graph <- function(object = NULL, #' @keywords internal #' @export keep_dbf_graph keep_dbf_graph <- function(object = NULL, - output_path = tempdir(), + output_path = NULL, name = NULL) { - ## Generate output path + if(is.null(output_path)){ + output_path <- tempdir() + dir.create(output_path, recursive = TRUE, showWarnings = FALSE) + } + # Get working directory if output_path is "." if (output_path == ".") { output_path <- getwd() } - # Check if output directory exists. If not stop the command. - if (!file.exists(output_path)) { - stop("Output directory provided does not exist.") + + if (!dir.exists(output_path)) { + dir.create(output_path, recursive = TRUE, showWarnings = FALSE) } # Create a random string if name is not provided diff --git a/man/construct_new_graph.Rd b/man/construct_new_graph.Rd index 7dc0986..22d84d9 100644 --- a/man/construct_new_graph.Rd +++ b/man/construct_new_graph.Rd @@ -4,7 +4,7 @@ \alias{construct_new_graph} \title{Construct a new graph for a ClusterSet object} \usage{ -construct_new_graph(object = NULL, k = 5, output_path = tempdir(), name = NULL) +construct_new_graph(object = NULL, k = 5, output_path = NULL, name = NULL) } \arguments{ \item{object}{A ClusterSet object.} diff --git a/man/gene_clustering.Rd b/man/gene_clustering.Rd index 795474d..49dda09 100644 --- a/man/gene_clustering.Rd +++ b/man/gene_clustering.Rd @@ -10,7 +10,7 @@ gene_clustering( inflation = 2, method = c("closest_neighborhood", "reciprocal_neighborhood"), threads = 1, - output_path = tempdir(), + output_path = NULL, name = NULL, keep_nn = FALSE ) diff --git a/man/keep_dbf_graph.Rd b/man/keep_dbf_graph.Rd index 9713fb1..0dc0934 100644 --- a/man/keep_dbf_graph.Rd +++ b/man/keep_dbf_graph.Rd @@ -4,7 +4,7 @@ \alias{keep_dbf_graph} \title{Construct a graph based on selected genes in a ClusterSet object and their neighbors} \usage{ -keep_dbf_graph(object = NULL, output_path = tempdir(), name = NULL) +keep_dbf_graph(object = NULL, output_path = NULL, name = NULL) } \arguments{ \item{object}{A ClusterSet object.} diff --git a/tests/testthat/test.dist2border.R b/tests/testthat/test.dist2border.R index 3989c25..fc93b26 100644 --- a/tests/testthat/test.dist2border.R +++ b/tests/testthat/test.dist2border.R @@ -1,6 +1,9 @@ library(Seurat) library(ggplot2) +# Set verbosity to 0 +set_verbosity(0) + load_example_dataset("7870305/files/lymph_node_tiny_2") identity <- Idents(lymph_node_tiny_2) classes <- ifelse(Idents(lymph_node_tiny_2) == 7, 1, 0) diff --git a/tests/testthat/test.gene_clustering.R b/tests/testthat/test.gene_clustering.R index 71a200f..b225bac 100644 --- a/tests/testthat/test.gene_clustering.R +++ b/tests/testthat/test.gene_clustering.R @@ -9,7 +9,7 @@ pbmc3k_medium_clust <- select_genes(data = pbmc3k_medium, test_that("Checking output slots generated by gene_clustering() using keep_nn as FALSE", { # Create output directory tmp_dir <- tempdir() - dir.create(tmp_dir) + dir.create(tmp_dir, recursive = TRUE, showWarnings = FALSE) ## A rather stringent version res_no_keep_nn <- gene_clustering(object = pbmc3k_medium_clust, From f3e40d7dd0392bd49262bffc7314d76523286018 Mon Sep 17 00:00:00 2001 From: dputhier Date: Fri, 22 Dec 2023 16:27:22 +0100 Subject: [PATCH 7/7] Updated html doc to . --- DESCRIPTION | 2 +- Makefile | 4 +- README.md | 14 +-- changelog.md | 4 + docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/articles/usage.html | 6 +- docs/authors.html | 6 +- docs/changelog.html | 5 +- docs/index.html | 93 +++++++++---------- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/ClusterSet-class.html | 6 +- docs/reference/check_format_cluster_set.html | 2 +- .../clust_names-ClusterSet-method.html | 2 +- docs/reference/clust_names.html | 2 +- .../clust_size-ClusterSet-method.html | 2 +- docs/reference/clust_size.html | 2 +- docs/reference/cluster_set_from_matrix.html | 2 +- docs/reference/cluster_set_from_seurat.html | 2 +- docs/reference/cluster_set_report.html | 8 +- .../cluster_set_to_xls-ClusterSet-method.html | 2 +- docs/reference/cluster_set_to_xls.html | 2 +- .../cluster_stats-ClusterSet-method.html | 2 +- docs/reference/cluster_stats.html | 2 +- .../col_names-ClusterSet-method.html | 2 +- docs/reference/col_names.html | 2 +- docs/reference/colors_for_gradient.html | 2 +- docs/reference/compare_genesets.html | 2 +- docs/reference/complex9.html | 2 +- docs/reference/complex9Noisy.html | 2 +- docs/reference/construct_new_graph.html | 6 +- docs/reference/create_3_rnd_clust.html | 2 +- docs/reference/create_4_rnd_clust.html | 2 +- docs/reference/create_rand_str.html | 2 +- docs/reference/dim-ClusterSet-method.html | 2 +- docs/reference/discrete_palette.html | 2 +- docs/reference/display_hull.html | 2 +- .../enrich_go-ClusterSet-method.html | 2 +- docs/reference/enrich_go.html | 2 +- docs/reference/filter_by_dot_prod.html | 2 +- docs/reference/filter_cluster_sd.html | 2 +- docs/reference/filter_cluster_size.html | 2 +- .../reference/filter_nb_supporting_cells.html | 2 +- .../gene_cluster-ClusterSet-method.html | 2 +- docs/reference/gene_cluster.html | 2 +- docs/reference/gene_clustering.html | 8 +- .../getFlippedTissueCoordinates.html | 2 +- docs/reference/get_data_for_scigenex.html | 2 +- docs/reference/get_genes.html | 2 +- docs/reference/get_verbosity.html | 2 +- ...in-grapes-character-ClusterSet-method.html | 2 +- .../grep_clust-ClusterSet-method.html | 2 +- docs/reference/grep_clust.html | 2 +- docs/reference/index.html | 2 +- docs/reference/install_mcl.html | 2 +- docs/reference/keep_dbf_graph.html | 8 +- docs/reference/load_example_dataset.html | 2 +- docs/reference/lymph_node_selected_spot.html | 2 +- .../reference/lymph_node_selected_spot_2.html | 2 +- docs/reference/mcl_system_cmd.html | 2 +- ...dule_quality_scores-ClusterSet-method.html | 2 +- docs/reference/module_quality_scores.html | 2 +- docs/reference/nclust-ClusterSet-method.html | 2 +- docs/reference/nclust.html | 2 +- docs/reference/ncol.ClusterSet.html | 2 +- docs/reference/nrow.ClusterSet.html | 2 +- ...t_clust_enrichments-ClusterSet-method.html | 2 +- docs/reference/plot_clust_enrichments.html | 2 +- docs/reference/plot_cluster_stats.html | 2 +- docs/reference/plot_cmp_genesets.html | 2 +- docs/reference/plot_dist.html | 2 +- .../plot_ggheatmap-ClusterSet-method.html | 2 +- docs/reference/plot_ggheatmap.html | 2 +- docs/reference/plot_heatmap.html | 2 +- ...markers_to_clusters-ClusterSet-method.html | 2 +- docs/reference/plot_markers_to_clusters.html | 2 +- docs/reference/plot_profiles.html | 2 +- docs/reference/plot_spatial.html | 2 +- docs/reference/plot_spatial_panel.html | 2 +- docs/reference/plot_stratum.html | 2 +- docs/reference/print_msg.html | 2 +- docs/reference/print_stat.html | 2 +- .../rename_clust-ClusterSet-method.html | 2 +- docs/reference/rename_clust.html | 2 +- .../reorder_clust-ClusterSet-method.html | 2 +- docs/reference/reorder_clust.html | 2 +- .../reorder_genes-ClusterSet-method.html | 2 +- docs/reference/reorder_genes.html | 2 +- .../row_names-ClusterSet-method.html | 2 +- docs/reference/row_names.html | 2 +- docs/reference/select_genes.html | 2 +- docs/reference/set_verbosity.html | 2 +- docs/reference/show-ClusterSet-method.html | 2 +- docs/reference/show_methods.html | 2 +- docs/reference/stratify_seurat.html | 2 +- .../sub-ClusterSet-ANY-ANY-ANY-method.html | 2 +- .../top_by_go-ClusterSet-method.html | 2 +- docs/reference/top_by_go.html | 2 +- .../top_genes-ClusterSet-method.html | 2 +- docs/reference/top_genes.html | 2 +- .../viz_enrich-ClusterSet-method.html | 2 +- docs/reference/viz_enrich.html | 2 +- .../which_clust-ClusterSet-method.html | 2 +- docs/reference/which_clust.html | 2 +- 105 files changed, 178 insertions(+), 176 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ae0a1ed..bbed0aa 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: scigenex Type: Package Title: The scigenex package (Single-Cell Informative GENe Explorer) -Version: 1.4.7 +Version: 1.4.8 Date: 2020-07-22 Author: J. Bavais, Sebastien Nin, Lionel Spinelli and Denis Puthier Maintainer: J. Bavais diff --git a/Makefile b/Makefile index f651d84..2ad46a2 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ MAKEFILE=Makefile -VERSION=1.4.7 +VERSION=1.4.8 .PHONY: help @@ -11,7 +11,7 @@ VERSION=1.4.7 help: @echo "" @echo "- Available targets:" - @echo "- Info: make check VERSION=1.4.2 " + @echo "- Info: make check VERSION=1.4.8 " @perl -ne 'if( /^(\w+):/){print "\t",$$1,"\n"}' $(MAKEFILE) @echo "" @echo "" diff --git a/README.md b/README.md index ec828a2..da3a411 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ - + + + ## ✔ Setting active project to '/Users/puthier/Documents/git/project_dev/scigenex' [![](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![Project Status: Active - The project has reached a stable, usable @@ -12,7 +14,7 @@ MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://cran.r-project. # SciGeneX repository -## :arrow_double_down: Installation +## :arrow\_double\_down: Installation ### System requirements @@ -49,7 +51,7 @@ You may skip this step as the latest versions of SciGeneX will call `scigenex::install_mcl()`to install MCL in `~/.scigenex` directory if this program is not found in the PATH. -#### Installation of MCL using install_mcl() +#### Installation of MCL using install\_mcl() The `install_mcl()` has been developed to ease MCL installation. This function should be call automatically from within R when calling the @@ -81,15 +83,15 @@ should be available in your PATH from within R. ## Example The scigenex library contains several datasets including the -pbmc3k_medium which is a subset from pbmc3k 10X dataset. +pbmc3k\_medium which is a subset from pbmc3k 10X dataset. library(Seurat) library(scigenex) set_verbosity(1) - + # Load a dataset load_example_dataset("7871581/files/pbmc3k_medium") - + # Select informative genes res <- select_genes(pbmc3k_medium, distance = "pearson", diff --git a/changelog.md b/changelog.md index 46ff9df..a5c1762 100644 --- a/changelog.md +++ b/changelog.md @@ -1,6 +1,10 @@ # Changelog +## v1.4.8 + +* Fix an issue with temp dir. + ## v1.4.7 * Change k_g argument to 's' in `gene_clustering()` function for clarity purpose. diff --git a/docs/404.html b/docs/404.html index 02dce74..842e6c5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/articles/index.html b/docs/articles/index.html index 3022ac7..90529f4 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/articles/usage.html b/docs/articles/usage.html index 707ae8b..cbee8c8 100644 --- a/docs/articles/usage.html +++ b/docs/articles/usage.html @@ -33,7 +33,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -193,7 +193,7 @@

Extracting gene modules using Sc ## * seed = 123 ## * keep_nn = FALSE ## * k_mcl_graph = 5 -## * output_path = /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmp6UgYV7 +## * output_path = /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpDSTiJs ## * name = s8gZ5uYQ33 ## * inflation = 2

There are various methods associated with the ClusterSet objects.

@@ -567,7 +567,7 @@

Session info## ## other attached packages: ## [1] tidyr_1.3.0 dplyr_1.1.3 -## [3] scigenex_1.4.7 stxKidney.SeuratData_0.1.0 +## [3] scigenex_1.4.8 stxKidney.SeuratData_0.1.0 ## [5] stxBrain.SeuratData_0.1.1 pbmc3k.SeuratData_3.1.4 ## [7] SeuratData_0.2.2 SeuratObject_4.1.3 ## [9] Seurat_4.3.0 patchwork_1.1.2 diff --git a/docs/authors.html b/docs/authors.html index 86ae2b0..2a3d53b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -66,13 +66,13 @@

Citation

Bavais J, Nin S, Spinelli L, Puthier D (2023). scigenex: The scigenex package (Single-Cell Informative GENe Explorer). -R package version 1.4.7, https://github.com/dputhier/scigenex. +R package version 1.4.8, https://github.com/dputhier/scigenex. 

@Manual{,
   title = {scigenex: The scigenex package (Single-Cell Informative GENe Explorer)},
   author = {J. Bavais and Sebastien Nin and Lionel Spinelli and Denis Puthier},
   year = {2023},
-  note = {R package version 1.4.7},
+  note = {R package version 1.4.8},
   url = {https://github.com/dputhier/scigenex},
 }
diff --git a/docs/changelog.html b/docs/changelog.html index 04156b5..bda981e 100644 --- a/docs/changelog.html +++ b/docs/changelog.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -51,6 +51,9 @@

Changelog

+

v1.4.8

+
  • Fix an issue with temp dir.
+

v1.4.7

  • Change k_g argument to ‘s’ in gene_clustering() function for clarity purpose.

  • Added dependency to DT library (required by cluster_set_report()).

    • diff --git a/docs/index.html b/docs/index.html index c60450b..ea6b81e 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ scigenex - 1.4.7 + 1.4.8
@@ -69,13 +69,14 @@
- +

+
## ✔ Setting active project to '/Users/puthier/Documents/git/project_dev/scigenex'
+

Project Status: Active - The project has reached a stable, usable state and is being actively developed. License: MIT

SciGeneX repository

-

-⏬ Installation +

:arrow_double_down: Installation

System requirements @@ -89,16 +90,16 @@

Step 1 - Installation of SciGeneXFrom R

The scigenex library is currently not available in CRAN or Bioc. To install from github, use:

-
devtools::install_github("dputhier/scigenex")
-library(scigenex)
+
devtools::install_github("dputhier/scigenex")
+library(scigenex)

From the terminal

Download the tar.gz from github or clone the main branch. Uncompress and run the following command from within the uncompressed scigenex folder:

-
R CMD INSTALL .
+
R CMD INSTALL .

Then load the library from within R.

-
library(scigenex)
+
library(scigenex)
@@ -114,22 +115,22 @@

Installation of MCL using install

Installation of MCL from source

One also can install MCL from source using the following code.

-
# Download the latest version of mcl 
-wget http://micans.org/mcl/src/mcl-latest.tar.gz
-# Uncompress and install mcl
-tar xvfz mcl-latest.tar.gz
-cd mcl-xx-xxx
-./configure
-make
-sudo make install
-# You should get mcl in your path
-mcl -h
+
# Download the latest version of mcl 
+wget http://micans.org/mcl/src/mcl-latest.tar.gz
+# Uncompress and install mcl
+tar xvfz mcl-latest.tar.gz
+cd mcl-xx-xxx
+./configure
+make
+sudo make install
+# You should get mcl in your path
+mcl -h

Installation of MCL from sources

Finally you may install MCL using conda. Importantly, the mcl command should be available in your PATH from within R.

-
conda install -c bioconda mcl
+
conda install -c bioconda mcl
@@ -137,28 +138,28 @@

Installation of MCL from sourcesExample

The scigenex library contains several datasets including the pbmc3k_medium which is a subset from pbmc3k 10X dataset.

-
library(Seurat)
-library(scigenex)
-set_verbosity(1)
-
-# Load a dataset
-load_example_dataset("7871581/files/pbmc3k_medium")
-
-# Select informative genes
-res <- select_genes(pbmc3k_medium,
-                     distance = "pearson",
-                     row_sum=5)
-                     
-# Cluster informative features
- 
-## Construct and partition the graph
-res <- gene_clustering(res, 
-                       inflation = 1.5, 
-                       threads = 4)
-                        
-# Display the heatmap of gene clusters
-res <- top_genes(res)
-plot_heatmap(res, cell_clusters = Seurat::Idents(pbmc3k_medium))
+
library(Seurat)
+library(scigenex)
+set_verbosity(1)
+
+# Load a dataset
+load_example_dataset("7871581/files/pbmc3k_medium")
+
+# Select informative genes
+res <- select_genes(pbmc3k_medium,
+                     distance = "pearson",
+                     row_sum=5)
+                     
+# Cluster informative features
+ 
+## Construct and partition the graph
+res <- gene_clustering(res, 
+                       inflation = 1.5, 
+                       threads = 4)
+                        
+# Display the heatmap of gene clusters
+res <- top_genes(res)
+plot_heatmap(res, cell_clusters = Seurat::Idents(pbmc3k_medium))

@@ -201,15 +202,7 @@

Developers

-
-

Dev status

-
    -
    • -
  • Project Status: Active - The project has reached a stable, usable state and is being actively developed.
    • -
  • License: MIT
    • -
    • -
-
+
diff --git a/docs/news/index.html b/docs/news/index.html index af7728e..cf07fa8 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 082de60..f0501ea 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: usage: usage.html -last_built: 2023-12-22T10:16Z +last_built: 2023-12-22T15:00Z urls: reference: https://scigenex.r-lib.org/reference article: https://scigenex.r-lib.org/articles diff --git a/docs/reference/ClusterSet-class.html b/docs/reference/ClusterSet-class.html index 15e9e22..03308fd 100644 --- a/docs/reference/ClusterSet-class.html +++ b/docs/reference/ClusterSet-class.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -123,7 +123,7 @@

Examples

#> |-- INFO : Computing distances to KNN. #> |-- INFO : Creating the input file for MCL algorithm. #> |-- INFO : Writing the input file. -#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/Rtmpd2nXJP/4qPd5kES06.input_mcl.txt'. +#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/RtmpBuBaBi/4qPd5kES06.input_mcl.txt'. #> |-- INFO : Adding results to a ClusterSet object. is(res) #> [1] "ClusterSet" @@ -213,7 +213,7 @@

Examples

#> * seed = 123 #> * keep_nn = FALSE #> * k_mcl_graph = 5 -#> * output_path = /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmpd2nXJP +#> * output_path = /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpBuBaBi #> * name = 4qPd5kES06 #> * inflation = 1.6 show_methods(res) diff --git a/docs/reference/check_format_cluster_set.html b/docs/reference/check_format_cluster_set.html index 5cf7308..7a2593c 100644 --- a/docs/reference/check_format_cluster_set.html +++ b/docs/reference/check_format_cluster_set.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/clust_names-ClusterSet-method.html b/docs/reference/clust_names-ClusterSet-method.html index a397655..3e5fb27 100644 --- a/docs/reference/clust_names-ClusterSet-method.html +++ b/docs/reference/clust_names-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/clust_names.html b/docs/reference/clust_names.html index 4d5ce31..fcd8b76 100644 --- a/docs/reference/clust_names.html +++ b/docs/reference/clust_names.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/clust_size-ClusterSet-method.html b/docs/reference/clust_size-ClusterSet-method.html index e050fe5..b06cd2d 100644 --- a/docs/reference/clust_size-ClusterSet-method.html +++ b/docs/reference/clust_size-ClusterSet-method.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/clust_size.html b/docs/reference/clust_size.html index cf4bcbd..fd2d01a 100644 --- a/docs/reference/clust_size.html +++ b/docs/reference/clust_size.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/cluster_set_from_matrix.html b/docs/reference/cluster_set_from_matrix.html index 52d7584..4a20f10 100644 --- a/docs/reference/cluster_set_from_matrix.html +++ b/docs/reference/cluster_set_from_matrix.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/cluster_set_from_seurat.html b/docs/reference/cluster_set_from_seurat.html index 06f2349..e2de18e 100644 --- a/docs/reference/cluster_set_from_seurat.html +++ b/docs/reference/cluster_set_from_seurat.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/cluster_set_report.html b/docs/reference/cluster_set_report.html index 73c8723..77a4b51 100644 --- a/docs/reference/cluster_set_report.html +++ b/docs/reference/cluster_set_report.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -151,10 +151,10 @@

Examples

#> |-- DEBUG : Report ID is : e5cde0b97ddfd882ccff69e313ef025a #> |-- INFO : Preparing report. #> |-- INFO : Dumping dataset -#> |-- INFO : Writing report into /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmpd2nXJP/scigenex_reportdeb41de8da24.Rmd -#> |-- INFO : Rmd file written at : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmpd2nXJP/scigenex_reportdeb41de8da24.Rmd +#> |-- INFO : Writing report into /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpBuBaBi/scigenex_report11b2d263f255f.Rmd +#> |-- INFO : Rmd file written at : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpBuBaBi/scigenex_report11b2d263f255f.Rmd #> |-- INFO : Rendering report. -#> |-- INFO : Creating report at : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmpd2nXJP/scigenex_reportdeb41de8da24.html +#> |-- INFO : Creating report at : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpBuBaBi/scigenex_report11b2d263f255f.html diff --git a/docs/reference/cluster_set_to_xls-ClusterSet-method.html b/docs/reference/cluster_set_to_xls-ClusterSet-method.html index 088b87c..3f8cd5d 100644 --- a/docs/reference/cluster_set_to_xls-ClusterSet-method.html +++ b/docs/reference/cluster_set_to_xls-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/cluster_set_to_xls.html b/docs/reference/cluster_set_to_xls.html index 436a664..92d750a 100644 --- a/docs/reference/cluster_set_to_xls.html +++ b/docs/reference/cluster_set_to_xls.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/cluster_stats-ClusterSet-method.html b/docs/reference/cluster_stats-ClusterSet-method.html index bef1fad..9500987 100644 --- a/docs/reference/cluster_stats-ClusterSet-method.html +++ b/docs/reference/cluster_stats-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/cluster_stats.html b/docs/reference/cluster_stats.html index 88406ee..326c9fb 100644 --- a/docs/reference/cluster_stats.html +++ b/docs/reference/cluster_stats.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/col_names-ClusterSet-method.html b/docs/reference/col_names-ClusterSet-method.html index 67750b6..d64be97 100644 --- a/docs/reference/col_names-ClusterSet-method.html +++ b/docs/reference/col_names-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/col_names.html b/docs/reference/col_names.html index 06eab1d..c59d73f 100644 --- a/docs/reference/col_names.html +++ b/docs/reference/col_names.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/colors_for_gradient.html b/docs/reference/colors_for_gradient.html index f6013ef..c5e8642 100644 --- a/docs/reference/colors_for_gradient.html +++ b/docs/reference/colors_for_gradient.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/compare_genesets.html b/docs/reference/compare_genesets.html index e4c544f..ebe1215 100644 --- a/docs/reference/compare_genesets.html +++ b/docs/reference/compare_genesets.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/complex9.html b/docs/reference/complex9.html index e29962c..7e1c5e5 100644 --- a/docs/reference/complex9.html +++ b/docs/reference/complex9.html @@ -22,7 +22,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/complex9Noisy.html b/docs/reference/complex9Noisy.html index 578b52a..f61ce1d 100644 --- a/docs/reference/complex9Noisy.html +++ b/docs/reference/complex9Noisy.html @@ -26,7 +26,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/construct_new_graph.html b/docs/reference/construct_new_graph.html index e149701..82e3496 100644 --- a/docs/reference/construct_new_graph.html +++ b/docs/reference/construct_new_graph.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -58,7 +58,7 @@

Construct a new graph for a ClusterSet object

- 
construct_new_graph(object = NULL, k = 5, output_path = tempdir(), name = NULL)
+ 
construct_new_graph(object = NULL, k = 5, output_path = NULL, name = NULL)
@@ -115,7 +115,7 @@

Examples

#> |-- INFO : Computing distances to KNN. #> |-- INFO : Creating the input file for MCL algorithm. #> |-- INFO : Writing the input file. -#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/Rtmpd2nXJP/06oFCM0di0.input_mcl.txt'. +#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/RtmpBuBaBi/06oFCM0di0.input_mcl.txt'.
diff --git a/docs/reference/create_3_rnd_clust.html b/docs/reference/create_3_rnd_clust.html index 5ea6e2e..38ddc3a 100644 --- a/docs/reference/create_3_rnd_clust.html +++ b/docs/reference/create_3_rnd_clust.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/create_4_rnd_clust.html b/docs/reference/create_4_rnd_clust.html index 7cb428c..e761361 100644 --- a/docs/reference/create_4_rnd_clust.html +++ b/docs/reference/create_4_rnd_clust.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/create_rand_str.html b/docs/reference/create_rand_str.html index a3c8ec6..1665475 100644 --- a/docs/reference/create_rand_str.html +++ b/docs/reference/create_rand_str.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/dim-ClusterSet-method.html b/docs/reference/dim-ClusterSet-method.html index 4b83c08..2763e6e 100644 --- a/docs/reference/dim-ClusterSet-method.html +++ b/docs/reference/dim-ClusterSet-method.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/discrete_palette.html b/docs/reference/discrete_palette.html index 5d06aaa..78a74f7 100644 --- a/docs/reference/discrete_palette.html +++ b/docs/reference/discrete_palette.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/display_hull.html b/docs/reference/display_hull.html index 230aa77..e003b1a 100644 --- a/docs/reference/display_hull.html +++ b/docs/reference/display_hull.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/enrich_go-ClusterSet-method.html b/docs/reference/enrich_go-ClusterSet-method.html index b13c8bf..c1239d4 100644 --- a/docs/reference/enrich_go-ClusterSet-method.html +++ b/docs/reference/enrich_go-ClusterSet-method.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/enrich_go.html b/docs/reference/enrich_go.html index 1f441c1..52736d0 100644 --- a/docs/reference/enrich_go.html +++ b/docs/reference/enrich_go.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/filter_by_dot_prod.html b/docs/reference/filter_by_dot_prod.html index b5a70a0..72c6a28 100644 --- a/docs/reference/filter_by_dot_prod.html +++ b/docs/reference/filter_by_dot_prod.html @@ -27,7 +27,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/filter_cluster_sd.html b/docs/reference/filter_cluster_sd.html index ba078ce..b2946ad 100644 --- a/docs/reference/filter_cluster_sd.html +++ b/docs/reference/filter_cluster_sd.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/filter_cluster_size.html b/docs/reference/filter_cluster_size.html index 666e8ce..83e4915 100644 --- a/docs/reference/filter_cluster_size.html +++ b/docs/reference/filter_cluster_size.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/filter_nb_supporting_cells.html b/docs/reference/filter_nb_supporting_cells.html index a8a127d..5502e41 100644 --- a/docs/reference/filter_nb_supporting_cells.html +++ b/docs/reference/filter_nb_supporting_cells.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/gene_cluster-ClusterSet-method.html b/docs/reference/gene_cluster-ClusterSet-method.html index 401a0a4..b9d7110 100644 --- a/docs/reference/gene_cluster-ClusterSet-method.html +++ b/docs/reference/gene_cluster-ClusterSet-method.html @@ -20,7 +20,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/gene_cluster.html b/docs/reference/gene_cluster.html index e1f6d09..c02c3d6 100644 --- a/docs/reference/gene_cluster.html +++ b/docs/reference/gene_cluster.html @@ -20,7 +20,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/gene_clustering.html b/docs/reference/gene_clustering.html index 3fd6c14..4fa4bf1 100644 --- a/docs/reference/gene_clustering.html +++ b/docs/reference/gene_clustering.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -66,7 +66,7 @@

Gene clustering using the Markov Cluster Algorithm (MCL) method.

inflation = 2, method = c("closest_neighborhood", "reciprocal_neighborhood"), threads = 1, - output_path = tempdir(), + output_path = NULL, name = NULL, keep_nn = FALSE ) @@ -153,7 +153,7 @@

Examples

#> |-- INFO : Computing distances to KNN. #> |-- INFO : Creating the input file for MCL algorithm. #> |-- INFO : Writing the input file. -#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/Rtmpd2nXJP/R14z6ff8TV.input_mcl.txt'. +#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/RtmpBuBaBi/R14z6ff8TV.input_mcl.txt'. #> |-- INFO : Adding results to a ClusterSet object. # Display the heatmap of gene clusters @@ -185,7 +185,7 @@

Examples

method="reciprocal_neighborhood") #> |-- INFO : Creating the input file for MCL algorithm. #> |-- INFO : Writing the input file. -#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/Rtmpd2nXJP/65vDYGyn24.input_mcl.txt'. +#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/RtmpBuBaBi/65vDYGyn24.input_mcl.txt'. #> |-- INFO : Adding results to a ClusterSet object. # Display the heatmap of gene clusters diff --git a/docs/reference/getFlippedTissueCoordinates.html b/docs/reference/getFlippedTissueCoordinates.html index 69b8461..672cac0 100644 --- a/docs/reference/getFlippedTissueCoordinates.html +++ b/docs/reference/getFlippedTissueCoordinates.html @@ -23,7 +23,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/get_data_for_scigenex.html b/docs/reference/get_data_for_scigenex.html index f7dd044..01730ac 100644 --- a/docs/reference/get_data_for_scigenex.html +++ b/docs/reference/get_data_for_scigenex.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/get_genes.html b/docs/reference/get_genes.html index 1cd5a13..0f2e95c 100644 --- a/docs/reference/get_genes.html +++ b/docs/reference/get_genes.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/get_verbosity.html b/docs/reference/get_verbosity.html index a47b26c..cbee8f1 100644 --- a/docs/reference/get_verbosity.html +++ b/docs/reference/get_verbosity.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/grapes-in-grapes-character-ClusterSet-method.html b/docs/reference/grapes-in-grapes-character-ClusterSet-method.html index 9ca2eb2..e88e05a 100644 --- a/docs/reference/grapes-in-grapes-character-ClusterSet-method.html +++ b/docs/reference/grapes-in-grapes-character-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/grep_clust-ClusterSet-method.html b/docs/reference/grep_clust-ClusterSet-method.html index a8a7af9..1480892 100644 --- a/docs/reference/grep_clust-ClusterSet-method.html +++ b/docs/reference/grep_clust-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/grep_clust.html b/docs/reference/grep_clust.html index a0a0b84..7e51886 100644 --- a/docs/reference/grep_clust.html +++ b/docs/reference/grep_clust.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/index.html b/docs/reference/index.html index fd26db8..dc4cee3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/install_mcl.html b/docs/reference/install_mcl.html index 3150d29..f49f79f 100644 --- a/docs/reference/install_mcl.html +++ b/docs/reference/install_mcl.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/keep_dbf_graph.html b/docs/reference/keep_dbf_graph.html index bbb9cdb..67fe070 100644 --- a/docs/reference/keep_dbf_graph.html +++ b/docs/reference/keep_dbf_graph.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 @@ -58,7 +58,7 @@

Construct a graph based on selected genes in a ClusterSet object and their n
- 
keep_dbf_graph(object = NULL, output_path = tempdir(), name = NULL)
+ 
keep_dbf_graph(object = NULL, output_path = NULL, name = NULL)
@@ -108,7 +108,7 @@

Examples

keep_dbf_graph(object = res) #> |-- INFO : Creating the input file for MCL algorithm. #> |-- INFO : Writing the input file. -#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/Rtmpd2nXJP/06oFCM0di0.input_mcl.txt'. +#> |-- INFO : The input file saved in '/var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/RtmpBuBaBi/06oFCM0di0.input_mcl.txt'. #> An object of class ClusterSet #> Name: 06oFCM0di0 #> Memory used: 1743336 @@ -132,7 +132,7 @@

Examples

#> * no_dknn_filter = FALSE #> * seed = 123 #> * keep_nn = TRUE -#> * output_path = /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//Rtmpd2nXJP +#> * output_path = /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T//RtmpBuBaBi #> * name = 06oFCM0di0
diff --git a/docs/reference/load_example_dataset.html b/docs/reference/load_example_dataset.html index 1fed1cb..9b42ab6 100644 --- a/docs/reference/load_example_dataset.html +++ b/docs/reference/load_example_dataset.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/lymph_node_selected_spot.html b/docs/reference/lymph_node_selected_spot.html index 6ff383e..a03b745 100644 --- a/docs/reference/lymph_node_selected_spot.html +++ b/docs/reference/lymph_node_selected_spot.html @@ -22,7 +22,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/lymph_node_selected_spot_2.html b/docs/reference/lymph_node_selected_spot_2.html index e737c8a..b338fd7 100644 --- a/docs/reference/lymph_node_selected_spot_2.html +++ b/docs/reference/lymph_node_selected_spot_2.html @@ -22,7 +22,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/mcl_system_cmd.html b/docs/reference/mcl_system_cmd.html index d262cab..6cea6fe 100644 --- a/docs/reference/mcl_system_cmd.html +++ b/docs/reference/mcl_system_cmd.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/module_quality_scores-ClusterSet-method.html b/docs/reference/module_quality_scores-ClusterSet-method.html index f586a6b..ed81eb7 100644 --- a/docs/reference/module_quality_scores-ClusterSet-method.html +++ b/docs/reference/module_quality_scores-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/module_quality_scores.html b/docs/reference/module_quality_scores.html index 6cd262c..9fff9ff 100644 --- a/docs/reference/module_quality_scores.html +++ b/docs/reference/module_quality_scores.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/nclust-ClusterSet-method.html b/docs/reference/nclust-ClusterSet-method.html index e257463..1864be0 100644 --- a/docs/reference/nclust-ClusterSet-method.html +++ b/docs/reference/nclust-ClusterSet-method.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/nclust.html b/docs/reference/nclust.html index 18f8430..22b2057 100644 --- a/docs/reference/nclust.html +++ b/docs/reference/nclust.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/ncol.ClusterSet.html b/docs/reference/ncol.ClusterSet.html index 40f253c..5e62b08 100644 --- a/docs/reference/ncol.ClusterSet.html +++ b/docs/reference/ncol.ClusterSet.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/nrow.ClusterSet.html b/docs/reference/nrow.ClusterSet.html index c5e3636..9b85fc6 100644 --- a/docs/reference/nrow.ClusterSet.html +++ b/docs/reference/nrow.ClusterSet.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_clust_enrichments-ClusterSet-method.html b/docs/reference/plot_clust_enrichments-ClusterSet-method.html index 0fe1194..dad33dc 100644 --- a/docs/reference/plot_clust_enrichments-ClusterSet-method.html +++ b/docs/reference/plot_clust_enrichments-ClusterSet-method.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_clust_enrichments.html b/docs/reference/plot_clust_enrichments.html index a184fc1..6823947 100644 --- a/docs/reference/plot_clust_enrichments.html +++ b/docs/reference/plot_clust_enrichments.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_cluster_stats.html b/docs/reference/plot_cluster_stats.html index 0a1ea90..4e3fed8 100644 --- a/docs/reference/plot_cluster_stats.html +++ b/docs/reference/plot_cluster_stats.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_cmp_genesets.html b/docs/reference/plot_cmp_genesets.html index 6ba2dc6..f9121ea 100644 --- a/docs/reference/plot_cmp_genesets.html +++ b/docs/reference/plot_cmp_genesets.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_dist.html b/docs/reference/plot_dist.html index 56f6d63..4426007 100644 --- a/docs/reference/plot_dist.html +++ b/docs/reference/plot_dist.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_ggheatmap-ClusterSet-method.html b/docs/reference/plot_ggheatmap-ClusterSet-method.html index a64c7ba..77daa4d 100644 --- a/docs/reference/plot_ggheatmap-ClusterSet-method.html +++ b/docs/reference/plot_ggheatmap-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_ggheatmap.html b/docs/reference/plot_ggheatmap.html index 09b4b9b..9676c3c 100644 --- a/docs/reference/plot_ggheatmap.html +++ b/docs/reference/plot_ggheatmap.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_heatmap.html b/docs/reference/plot_heatmap.html index 2f73b60..61b045f 100644 --- a/docs/reference/plot_heatmap.html +++ b/docs/reference/plot_heatmap.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_markers_to_clusters-ClusterSet-method.html b/docs/reference/plot_markers_to_clusters-ClusterSet-method.html index 79e7821..ce2d7a8 100644 --- a/docs/reference/plot_markers_to_clusters-ClusterSet-method.html +++ b/docs/reference/plot_markers_to_clusters-ClusterSet-method.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_markers_to_clusters.html b/docs/reference/plot_markers_to_clusters.html index c49d030..d1d3658 100644 --- a/docs/reference/plot_markers_to_clusters.html +++ b/docs/reference/plot_markers_to_clusters.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_profiles.html b/docs/reference/plot_profiles.html index 467434e..0a51475 100644 --- a/docs/reference/plot_profiles.html +++ b/docs/reference/plot_profiles.html @@ -18,7 +18,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_spatial.html b/docs/reference/plot_spatial.html index 708deaa..e5a6da0 100644 --- a/docs/reference/plot_spatial.html +++ b/docs/reference/plot_spatial.html @@ -21,7 +21,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_spatial_panel.html b/docs/reference/plot_spatial_panel.html index 396df41..db07c89 100644 --- a/docs/reference/plot_spatial_panel.html +++ b/docs/reference/plot_spatial_panel.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/plot_stratum.html b/docs/reference/plot_stratum.html index 781f2f9..fec2f95 100644 --- a/docs/reference/plot_stratum.html +++ b/docs/reference/plot_stratum.html @@ -17,7 +17,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/print_msg.html b/docs/reference/print_msg.html index af9ddc5..6d040d4 100644 --- a/docs/reference/print_msg.html +++ b/docs/reference/print_msg.html @@ -17,7 +17,7 @@ scigenex - 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1.4.7 + 1.4.8 diff --git a/docs/reference/stratify_seurat.html b/docs/reference/stratify_seurat.html index 0287c95..8f86847 100644 --- a/docs/reference/stratify_seurat.html +++ b/docs/reference/stratify_seurat.html @@ -20,7 +20,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/sub-ClusterSet-ANY-ANY-ANY-method.html b/docs/reference/sub-ClusterSet-ANY-ANY-ANY-method.html index b18ae3c..fc2ba52 100644 --- a/docs/reference/sub-ClusterSet-ANY-ANY-ANY-method.html +++ b/docs/reference/sub-ClusterSet-ANY-ANY-ANY-method.html @@ -20,7 +20,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/top_by_go-ClusterSet-method.html b/docs/reference/top_by_go-ClusterSet-method.html index 8f84ac9..2899418 100644 --- a/docs/reference/top_by_go-ClusterSet-method.html +++ b/docs/reference/top_by_go-ClusterSet-method.html @@ -19,7 +19,7 @@ scigenex - 1.4.7 + 1.4.8 diff --git a/docs/reference/top_by_go.html b/docs/reference/top_by_go.html index 46e318c..22e468b 100644 --- a/docs/reference/top_by_go.html +++ b/docs/reference/top_by_go.html @@ -19,7 +19,7 @@ scigenex - 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