fixed test error

ajitjohnson · Dec 25, 2020 · c00517e · c00517e
1 parent 42954b6
commit c00517e
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Showing 15 changed files with 41 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: imsig
 Type: Package
 Title: Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
-Version: 1.1.0
+Version: 1.1.1
 Author: Ajit Johnson Nirmal
 Maintainer: Ajit Johnson Nirmal <[email protected]>
 Description: Estimate the relative abundance of tissue-infiltrating immune subpopulations abundances using gene expression data. 
@@ -17,5 +17,5 @@ Imports:
   ggplot2 (>= 2.2),
   gridExtra (>= 2.3),
   survival (>= 2.4)
-RoxygenNote: 6.0.1
+RoxygenNote: 7.1.1
 Suggests: testthat
diff --git a/R/imsig.R b/R/imsig.R
@@ -6,7 +6,7 @@
 #' @param sort_by Can be used to sort the samples by predicted abundance of a particular cell type. All other cell types follow this sorting. By default it is sorted by `T cells`
 #' @return Relative abundance of immune cells across samples. Returns a dataframe.
 #' @examples
-#' cell_abundance = imsig (exp = example_data, r = 0.7)
+#' cell_abundance = imsig (exp = example_data, r = 0.7, sort=TRUE, sort_by='T cells')
 #' head(cell_abundance)
 #' @seealso \code{\link{feature_select}}, \code{\link{example_data}}
 #' @export

diff --git a/R/imsig_survival.R b/R/imsig_survival.R
@@ -7,7 +7,7 @@
 #' @param r Use a value between 0 and 1. Default is 0.6. This is a user defined correlation cut-off to perform feature selection (\code{\link{feature_select}}). Feature selection aids to enrich the prediction of relative abundance of immune cells by filtering off poorly correlated ImSig genes. To get an idea of what cut-off to use check the results of (\code{\link{gene_stat}}) and choose a cut-off that displays high median correlation and maintains a high proportion of genes after feature selection.
 #' @return Hazard Ratio
 #' @examples \donttest{
-#' survival = imsig_survival (exp = example_data)
+#' survival = imsig_survival (exp = example_data, cli = example_cli)
 #' head(survival)
 #' }
 #' @import survival
@@ -25,7 +25,7 @@ imsig_survival <- function(exp, cli, time = 'time', status= 'status', r = 0.6){
   for (i in 1: length(levels(sig$cell))){
     cell_ordered <- cell_cli[sort.list(cell_cli[,i]),]
     cell_ordered$group <- ifelse(cell_ordered[,i] <= median(cell_cli[,i]), "low", "high")
-    cox <- coxph(Surv(time, status) ~ group, cell_ordered)
+    cox <- survival::coxph(Surv(time, status) ~ group, cell_ordered)
     x <- summary(cox)[8]
     HR.OS <- data.frame(log2(x[[1]][1]))
     HR.UP <- data.frame(log2(x[[1]][4]))

diff --git a/man/corr_matrix.Rd b/man/corr_matrix.Rd
diff --git a/man/example_cli.Rd b/man/example_cli.Rd
diff --git a/man/example_data.Rd b/man/example_data.Rd
diff --git a/man/feature_select.Rd b/man/feature_select.Rd
diff --git a/man/gene_stat.Rd b/man/gene_stat.Rd
diff --git a/man/imsig.Rd b/man/imsig.Rd
diff --git a/man/imsig_survival.Rd b/man/imsig_survival.Rd
diff --git a/man/plot_abundance.Rd b/man/plot_abundance.Rd
diff --git a/man/plot_network.Rd b/man/plot_network.Rd
diff --git a/man/plot_survival.Rd b/man/plot_survival.Rd
diff --git a/man/sig.Rd b/man/sig.Rd
diff --git a/tests/testthat/test_imsig.R b/tests/testthat/test_imsig.R
@@ -1,2 +1,2 @@
-cell_abundance = imsig (exp = example_data, r = 0.7)
+cell_abundance = imsig (exp = example_data, r = 0.7, sort=TRUE, sort_by='T cells')
 head(cell_abundance)