From 32ef0d7fbd8a6419f1d1d3ddf498eb24d6ba5484 Mon Sep 17 00:00:00 2001 From: aduvermy <arnaud.duvermy@ens-lyon.fr> Date: Wed, 24 Jan 2024 09:50:43 +0100 Subject: [PATCH] rebuild packg modifying seqDepth scaling method --- R/evaluation_identity.R | 1 + R/mock_rnaseq.R | 3 +-- R/prepare_data2fit.R | 4 ++-- man/eval_identityTerm.Rd | 2 ++ man/getColumnWithSampleID.Rd | 2 +- man/prepareData2fit.Rd | 2 +- pkgdown/_pkgdown.yml | 6 +----- tests/testthat/test-prepare_data2fit.R | 4 ++-- 8 files changed, 11 insertions(+), 13 deletions(-) diff --git a/R/evaluation_identity.R b/R/evaluation_identity.R index 5053828..76d9efa 100644 --- a/R/evaluation_identity.R +++ b/R/evaluation_identity.R @@ -61,6 +61,7 @@ get_rsquare_2plot <- function(data_rsquare){ #' #' @param data_identity A data frame containing comparison results with "actual" and "estimate" columns. #' @param palette_color dict-like palette default: palette_color = c(DESeq2 = "#500472", HTRfit ="#79cbb8") +#' @param palette_shape Optional parameter that sets the point shape for plots.Default : c(DESeq2 = 17, HTRfit = 19). #' @param ... additional parameters to pass geom_point aes #' @return A ggplot2 identity plot and R2 metric associated #' diff --git a/R/mock_rnaseq.R b/R/mock_rnaseq.R index 8f60f98..a2227cd 100644 --- a/R/mock_rnaseq.R +++ b/R/mock_rnaseq.R @@ -96,8 +96,7 @@ mock_rnaseq <- function(list_var, n_genes, min_replicates, max_replicates, seque if (!is.null(sequencing_depth)) { message("Scaling count table according to sequencing depth.") - message("Scaling count table according to sequencing depth.") - + message("Scaling counts by sequencing depth may exhibit some randomness due to certain parameter combinations, resulting in erratic behavior. This can be minimized by simulating more genes. We advise verifying the simulated sequencing depth to avoid drawing incorrect conclusions.") mu_ij_dtf_rep <- scaleCountsTable(mu_ij_matx_rep, sequencing_depth) mu_ij_matx_rep <- as.matrix(mu_ij_dtf_rep) } diff --git a/R/prepare_data2fit.R b/R/prepare_data2fit.R index e2cdd24..482c5b3 100644 --- a/R/prepare_data2fit.R +++ b/R/prepare_data2fit.R @@ -34,7 +34,7 @@ countMatrix_2longDtf <- function(countMatrix, value_name = "kij", id_vars = "gen #' @export #' @examples #' list_var <- init_variable() -#' mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2, 2) +#' mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2) #' dtf_countLong <- countMatrix_2longDtf(mock_data$counts) #' getColumnWithSampleID(dtf_countLong, mock_data$metadata) getColumnWithSampleID <- function(dtf_countsLong, metadata) { @@ -67,7 +67,7 @@ getColumnWithSampleID <- function(dtf_countsLong, metadata) { #' @export #' @examples #' list_var <- init_variable() -#' mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2, 2) +#' mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2) #' data2fit <- prepareData2fit(mock_data$counts, mock_data$metadata) prepareData2fit <- function(countMatrix, metadata, normalization = TRUE , response_name = "kij", groupID = "geneID" ) { diff --git a/man/eval_identityTerm.Rd b/man/eval_identityTerm.Rd index 07a47ad..faa4403 100644 --- a/man/eval_identityTerm.Rd +++ b/man/eval_identityTerm.Rd @@ -16,6 +16,8 @@ eval_identityTerm( \item{palette_color}{dict-like palette default: palette_color = c(DESeq2 = "#500472", HTRfit ="#79cbb8")} +\item{palette_shape}{Optional parameter that sets the point shape for plots.Default : c(DESeq2 = 17, HTRfit = 19).} + \item{...}{additional parameters to pass geom_point aes} } \value{ diff --git a/man/getColumnWithSampleID.Rd b/man/getColumnWithSampleID.Rd index 288ba87..9439edb 100644 --- a/man/getColumnWithSampleID.Rd +++ b/man/getColumnWithSampleID.Rd @@ -19,7 +19,7 @@ Returns the column name in the metadata data frame that corresponds to the given } \examples{ list_var <- init_variable() -mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2, 2) +mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2) dtf_countLong <- countMatrix_2longDtf(mock_data$counts) getColumnWithSampleID(dtf_countLong, mock_data$metadata) } diff --git a/man/prepareData2fit.Rd b/man/prepareData2fit.Rd index 4158249..94555f4 100644 --- a/man/prepareData2fit.Rd +++ b/man/prepareData2fit.Rd @@ -34,6 +34,6 @@ Prepares the countMatrix and metadata for fitting by converting the countMatrix } \examples{ list_var <- init_variable() - mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2, 2) + mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2) data2fit <- prepareData2fit(mock_data$counts, mock_data$metadata) } diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index 21b84db..58de1b1 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -3,7 +3,7 @@ repo: home: https://gitbio.ens-lyon.fr/LBMC/yvertlab/vortex/plasticity_mutation/HTRfit navbar: structure: - left: [home, intro, reference, articles, additionalPArt ,news] + left: [home, intro, reference, articles ,news] right: [search , gitlab] components: gitlab: @@ -18,10 +18,6 @@ template: includes: in_header: <script defer data-domain="pkgdown.r-lib.org,all.tidyverse.org" src="https://plausible.io/js/plausible.js"></script> - -additionalPArt: -- title: Testing - news: releases: - text: "Version 2.0.0" diff --git a/tests/testthat/test-prepare_data2fit.R b/tests/testthat/test-prepare_data2fit.R index b288e61..beb3720 100644 --- a/tests/testthat/test-prepare_data2fit.R +++ b/tests/testthat/test-prepare_data2fit.R @@ -21,7 +21,7 @@ test_that("countMatrix_2longDtf converts count matrix to long data frame", { test_that("getColumnWithSampleID returns column name with sampleID", { # dummy data list_var <- init_variable() - mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2, 2) + mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2) dtf_countLong <- countMatrix_2longDtf(mock_data$counts) # Expected output @@ -38,7 +38,7 @@ test_that("getColumnWithSampleID returns column name with sampleID", { test_that("prepareData2fit prepares data for fitting", { # dummy data list_var <- init_variable() - mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2, 2) + mock_data <- mock_rnaseq(list_var, n_genes = 3, 2,2) # Prepare data for fitting data2fit <- prepareData2fit(mock_data$counts, mock_data$metadata) -- GitLab