Hello!
I am trying to create correlation heatmaps for the example data but unable to do so on R and run into the following error:
OPTION 1) - Heatmap specifying pearson distance and an overview
My code:
mSet<-PlotCorrHeatMap(mSet, “corr_0_”, format = “png”, dpi = 300, width=NA,
“col”, “pearson”, “bwm”, “overview”, F, F, 0.0)
Console:
#[1] 0 0
#Error in if (fix.col) { : argument is not interpretable as logical
OPTION 2) - Heatmap specifying pearson correlation and a detailed view
My code:
mSet<-PlotCorrHeatMap(mSet, “corr_1_”, format = “png”, dpi=300, width=NA,
“col”, “spearman”, “bwm”, “detail”, F, F, 999)
Console:
#[1] 0 999
#Error in if (fix.col) { : argument is not interpretable as logical
My session information:
sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] iheatmapr_0.7.1 memoise_2.0.1 ggplot2_3.5.1 scales_1.3.0
[5] Rserve_1.8-13 MetaboAnalystR_4.0.0 devtools_2.4.5 usethis_2.2.3
loaded via a namespace (and not attached):
[1] fastmatch_1.1-4 plyr_1.8.9 igraph_2.0.3 lazyeval_0.2.2
[5] splines_4.2.0 RApiSerialize_0.1.3 BiocParallel_1.30.4 listenv_0.9.1
[9] digest_0.6.36 foreach_1.5.2 htmltools_0.5.8.1 fansi_1.0.6
[13] magrittr_2.0.3 limma_3.52.4 remotes_2.5.0 fastcluster_1.2.6
[17] recipes_1.1.0 globals_0.16.3 gower_1.0.1 RcppParallel_5.1.8
[21] hardhat_1.4.0 timechange_0.3.0 siggenes_1.70.0 colorspace_2.1-0
[25] blob_1.2.4 ggrepel_0.9.5 xfun_0.45 dplyr_1.1.4
[29] callr_3.7.6 jsonlite_1.8.8 stringfish_0.16.0 impute_1.70.0
[33] survival_3.7-0 iterators_1.0.14 glue_1.7.0 gtable_0.3.5
[37] ipred_0.9-14 pkgbuild_1.4.4 future.apply_1.11.2 BiocGenerics_0.42.0
[41] DBI_1.2.3 edgeR_3.38.4 miniUI_0.1.1.1 Rcpp_1.0.12
[45] viridisLite_0.4.2 xtable_1.8-4 bit_4.0.5 preprocessCore_1.58.0
[49] stats4_4.2.0 lava_1.8.0 prodlim_2024.06.25 profvis_0.3.8
[53] htmlwidgets_1.6.4 httr_1.4.7 fgsea_1.22.0 gplots_3.1.3.1
[57] RColorBrewer_1.1-3 ellipsis_0.3.2 urlchecker_1.0.1 pkgconfig_2.0.3
[61] farver_2.1.2 nnet_7.3-19 locfit_1.5-9.10 utf8_1.2.4
[65] caret_6.0-94 tidyselect_1.2.1 labeling_0.4.3 rlang_1.1.4
[69] reshape2_1.4.4 later_1.3.2 munsell_0.5.1 tools_4.2.0
[73] cachem_1.1.0 cli_3.6.3 generics_0.1.3 RSQLite_2.3.7
[77] stringr_1.5.1 fastmap_1.2.0 knitr_1.48 ModelMetrics_1.2.2.2
[81] processx_3.8.4 bit64_4.0.5 fs_1.6.4 caTools_1.18.2
[85] crmn_0.0.21 scrime_1.3.5 purrr_1.0.2 glasso_1.11
[89] future_1.33.2 nlme_3.1-165 mime_0.12 compiler_4.2.0
[93] rstudioapi_0.16.0 plotly_4.10.4 curl_5.2.1 tibble_3.2.1
[97] stringi_1.8.4 ps_1.7.7 desc_1.4.3 lattice_0.22-6
[101] Matrix_1.5-3 multtest_2.52.0 vctrs_0.6.5 pillar_1.9.0
[105] lifecycle_1.0.4 data.table_1.15.4 cowplot_1.1.3 bitops_1.0-7
[109] httpuv_1.6.15 R6_2.5.1 pcaMethods_1.88.0 qs_0.26.3
[113] promises_1.3.0 KernSmooth_2.23-24 gridExtra_2.3 parallelly_1.37.1
[117] sessioninfo_1.2.2 codetools_0.2-20 MASS_7.3-56 gtools_3.9.5
[121] pkgload_1.4.0 withr_3.0.0 parallel_4.2.0 grid_4.2.0
[125] rpart_4.1.23 timeDate_4032.109 tidyr_1.3.1 class_7.3-22
[129] Cairo_1.6-2 pROC_1.18.5 Biobase_2.56.0 shiny_1.8.1.1
[133] lubridate_1.9.3
Thank you for your guidance on how to fix this error!