{"comment":{"url":"https://api.github.com/repos/hbc/bcbioSinglecell/comments/22740336","html_url":"https://github.com/hbc/bcbioSinglecell/commit/d63611240f3f14be2bdcb174c505fee725c6e793#commitcomment-22740336","id":22740336,"user":{"login":"lintr-bot","id":10925265,"avatar_url":"https://avatars0.githubusercontent.com/u/10925265?v=3","gravatar_id":"","url":"https://api.github.com/users/lintr-bot","html_url":"https://github.com/lintr-bot","followers_url":"https://api.github.com/users/lintr-bot/followers","following_url":"https://api.github.com/users/lintr-bot/following{/other_user}","gists_url":"https://api.github.com/users/lintr-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/lintr-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lintr-bot/subscriptions","organizations_url":"https://api.github.com/users/lintr-bot/orgs","repos_url":"https://api.github.com/users/lintr-bot/repos","events_url":"https://api.github.com/users/lintr-bot/events{/privacy}","received_events_url":"https://api.github.com/users/lintr-bot/received_events","type":"User","site_admin":false},"position":null,"line":null,"path":null,"commit_id":"d63611240f3f14be2bdcb174c505fee725c6e793","created_at":"2017-06-24T11:03:42Z","updated_at":"2017-06-24T11:03:42Z","body":"[R/bcbioSinglecell.R:20:12:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/bcbioSinglecell.R#L20) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​bins <- 100\n        ~~~^\n```\n[R/deprecated.R:23:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L23) *warning:* **no visible global function definition for 'aggregate_sparse_features'**\n```r\n​    aggregate_sparse_features(...)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/deprecated.R:32:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L32) *warning:* **no visible global function definition for 'aggregate_sparse_replicates'**\n```r\n​    aggregate_sparse_replicates(...)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/deprecated.R:59:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L59) *warning:* **no visible global function definition for 'read_csv_with_rownames', Did you mean 'load_csv_with_rownames'?**\n```r\n​    read_csv_with_rownames(...)\n    ^~~~~~~~~~~~~~~~~~~~~~\n```\n[R/deprecated.R:68:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L68) *warning:* **no visible global function definition for 'read_counts'**\n```r\n​    read_counts(...)\n    ^~~~~~~~~~~\n```\n[R/deprecated.R:77:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L77) *warning:* **no visible global function definition for 'create_bcbio_skeleton'**\n```r\n​    create_bcbio_skeleton(...)\n    ^~~~~~~~~~~~~~~~~~~~~\n```\n[R/deprecated.R:95:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L95) *warning:* **no visible global function definition for 'plot_mito_ratio_boxplot'**\n```r\n​    plot_mito_ratio_boxplot(...)\n    ^~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/deprecated.R:104:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L104) *warning:* **no visible global function definition for 'plot_mito_ratio_histogram'**\n```r\n​    plot_mito_ratio_histogram(...)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/deprecated.R:113:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L113) *warning:* **no visible global function definition for 'plot_mito_ratio_scatterplot'**\n```r\n​    plot_mito_ratio_scatterplot(...)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/deprecated.R:149:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/deprecated.R#L149) *warning:* **no visible global function definition for 'read_10x'**\n```r\n​    read_10x(...)\n    ^~~~~~~~\n```\n[R/internal-annotables.R:51:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-annotables.R#L51) *warning:* **local variable 'coding' assigned but may not be used**\n```r\n​    coding <- c(\"protein_coding\")\n    ^~~~~~\n```\n[R/internal-annotables.R:51:15:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-annotables.R#L51) *warning:* **Unneded concatenation of a constant. Remove the \"c\" call.**\n```r\n​    coding <- c(\"protein_coding\")\n              ^\n```\n[R/internal-annotables.R:52:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-annotables.R#L52) *warning:* **local variable 'decaying' assigned but may not be used**\n```r\n​    decaying <- c(\"non_stop_decay\", \"nonsense_mediated_decay\")\n    ^~~~~~~~\n```\n[R/internal-annotables.R:53:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-annotables.R#L53) *warning:* **local variable 'noncoding' assigned but may not be used**\n```r\n​    noncoding <- c(\"known_ncrna\", \"lincRNA\", \"non_coding\")\n    ^~~~~~~~~\n```\n[R/internal-bcbio_counts.R:17:40:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-bcbio_counts.R#L17) *warning:* **no visible binding for global variable 'ensembl'**\n```r\n​    indexes <- match(rownames(counts), ensembl[[\"ensembl_transcript_id\"]])\n                                       ^~~~~~~\n```\n[R/internal-bcbio_counts.R:21:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-bcbio_counts.R#L21) *warning:* **no visible global function definition for '.aggregate_sparse_features'**\n```r\n​    .aggregate_sparse_features(counts, gene_names)\n    ^~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal-metrics.R:30:11:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-metrics.R#L30) *style:* **Commented code should be removed.**\n```r\n​        # Rowname: `file_name` + `sample_barcode` + `cellular_barcode`\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal-metrics.R:33:59:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-metrics.R#L33) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        genes_detected = Matrix::colSums(sparse_counts > 0),\n                                                         ~^\n```\n[R/internal-sparse_counts.R:41:11:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-sparse_counts.R#L41) *style:* **Commented code should be removed.**\n```r\n​        # matrix_file <- gunzip(matrix_file)\n          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal-sparse_counts.R:97:26:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-sparse_counts.R#L97) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    if (any(is.na(tx2gene$enstxp))) stop(\"Unmapped transcripts present\")\n                         ^\n```\n[R/internal-tenx.R:62:46:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-tenx.R#L62) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        rownames(counts) <- make.unique(genes$external_gene_name)\n                                             ^\n```\n[R/internal-tx2symbol.R:18:19:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-tx2symbol.R#L18) *warning:* **no visible global function definition for 'strip_transcript_versions'**\n```r\n​        matrix <- strip_transcript_versions(matrix)\n                  ^~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/internal-tx2symbol.R:22:31:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-tx2symbol.R#L22) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    rownames(matrix) <- lookup$to\n                              ^\n```\n[R/internal-unlist_barcodes.R:12:20:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-unlist_barcodes.R#L12) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    barcodes <- run$barcodes\n                   ^\n```\n[R/internal-unlist_barcodes.R:20:45:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-unlist_barcodes.R#L20) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​            mutate(log10_reads = log10(.data$reads),\n                                            ^\n```\n[R/internal-unlist_barcodes.R:22:10:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-unlist_barcodes.R#L22) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**\n```r\n​    }) %>% bind_rows %>%\n       ~~^\n```\n[R/internal-unlist_barcodes.R:23:22:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/internal-unlist_barcodes.R#L23) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        left_join(run$metadata[, c(\"sample_barcode\", \"sample_name\")],\n                     ^\n```\n[R/load_cellranger.R:4:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/load_cellranger.R#L4) *warning:* **local variable 'umi_type' assigned but may not be used**\n```r\n​    umi_type <- \"chromium_v2\"\n    ^~~~~~~~\n```\n[R/load_run.R:36:33:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/load_run.R#L36) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​    if (length(project_dir) != 1) {\n                               ~^\n```\n[R/load_run.R:42:5:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/load_run.R#L42) *warning:* **local variable 'template' assigned but may not be used**\n```r\n​    template <- match[[3L]]\n    ^~~~~~~~\n```\n[R/methods-filter.R:23:17:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/methods-filter.R#L23) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​    reads = 1000,\n            ~~~~^\n```\n[R/methods-filter.R:24:20:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/methods-filter.R#L24) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​    min_genes = 500,\n                ~~~^\n```\n[R/methods-filter.R:25:21:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/methods-filter.R#L25) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​    max_genes = 5000,\n                ~~~~^\n```\n[R/methods-top_barcodes.R:10:67:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/methods-top_barcodes.R#L10) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​setMethod(\"top_barcodes\", \"bcbioSCDataSet\", function(object, n = 2) {\n                                                                 ~^\n```\n[R/plot-metrics.R:20:21:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L20) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    if (!is.null(run$lanes)) {\n                    ^\n```\n[R/plot-metrics.R:21:20:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L21) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        plot <- run$metrics %>%\n                   ^\n```\n[R/plot-metrics.R:22:26:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L22) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​            left_join(run$metadata,\n                         ^\n```\n[R/plot-metrics.R:32:20:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L32) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        plot <- run$metrics %>%\n                   ^\n```\n[R/plot-metrics.R:66:19:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L66) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    metrics <- run$metrics %>%\n                  ^\n```\n[R/plot-metrics.R:97:19:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L97) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    metrics <- run$metrics %>%\n                  ^\n```\n[R/plot-metrics.R:108:28:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L108) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        expand_limits(x = 0) +\n                          ~^\n```\n[R/plot-metrics.R:111:50:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L111) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                               ~~^\n```\n[R/plot-metrics.R:111:61:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L111) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                                           ~^\n```\n[R/plot-metrics.R:127:16:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L127) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    plot <- run$metrics %>%\n               ^\n```\n[R/plot-metrics.R:139:33:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L139) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​                             run$metrics,\n                                ^\n```\n[R/plot-metrics.R:144:28:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L144) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        expand_limits(y = 0) +\n                          ~^\n```\n[R/plot-metrics.R:146:50:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L146) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                               ~~^\n```\n[R/plot-metrics.R:146:61:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L146) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                                           ~^\n```\n[R/plot-metrics.R:158:16:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L158) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    plot <- run$metrics %>%\n               ^\n```\n[R/plot-metrics.R:167:28:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L167) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        expand_limits(x = 0) +\n                          ~^\n```\n[R/plot-metrics.R:169:50:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L169) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                               ~~^\n```\n[R/plot-metrics.R:169:61:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L169) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                                           ~^\n```\n[R/plot-metrics.R:182:47:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L182) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​plot_genes_detected <- function(run, min = 500, max = NULL) {\n                                           ~~~^\n```\n[R/plot-metrics.R:195:24:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L195) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        intgroup <- run$intgroup[1]\n                       ^\n```\n[R/plot-metrics.R:195:33:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L195) *warning:* **Use `[[` instead of `[`  to extract an element.**\n```r\n​        intgroup <- run$intgroup[1]\n                                ^\n```\n[R/plot-metrics.R:195:35:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L195) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        intgroup <- run$intgroup[1]\n                                 ~^\n```\n[R/plot-metrics.R:197:8:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L197) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    run$metrics %>%\n       ^\n```\n[R/plot-metrics.R:213:50:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L213) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                               ~~^\n```\n[R/plot-metrics.R:213:61:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L213) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                                           ~^\n```\n[R/plot-metrics.R:221:8:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L221) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    run$metrics %>%\n       ^\n```\n[R/plot-metrics.R:234:33:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L234) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​                             run$metrics,\n                                ^\n```\n[R/plot-metrics.R:236:55:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L236) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            aes_(label = ~round(mito_ratio, digits = 2)),\n                                                     ~^\n```\n[R/plot-metrics.R:240:28:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L240) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        expand_limits(y = 0) +\n                          ~^\n```\n[R/plot-metrics.R:242:50:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L242) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                               ~~^\n```\n[R/plot-metrics.R:242:61:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L242) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                                           ~^\n```\n[R/plot-metrics.R:247:8:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L247) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    run$metrics %>%\n       ^\n```\n[R/plot-metrics.R:256:15:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L256) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        xlim(0, 1) +\n             ~^\n```\n[R/plot-metrics.R:256:18:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L256) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        xlim(0, 1) +\n                ~^\n```\n[R/plot-metrics.R:259:50:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L259) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                               ~~^\n```\n[R/plot-metrics.R:259:61:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L259) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                                           ~^\n```\n[R/plot-metrics.R:264:8:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L264) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    run$metrics %>%\n       ^\n```\n[R/plot-metrics.R:275:50:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L275) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                               ~~^\n```\n[R/plot-metrics.R:275:61:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L275) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​            axis.text.x = element_text(angle = 90, hjust = 1),\n                                                           ~^\n```\n[R/plot-metrics.R:291:8:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L291) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    run$metrics %>%\n       ^\n```\n[R/plot-metrics.R:303:33:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L303) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​                             run$metrics,\n                                ^\n```\n[R/plot-metrics.R:308:28:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L308) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        expand_limits(y = 0) +\n                          ~^\n```\n[R/plot-metrics.R:315:8:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plot-metrics.R#L315) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    run$metrics %>%\n       ^\n```\n[R/plots-barcodes.R:7:20:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L7) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​    barcodes <- bcb$barcodes\n                   ^\n```\n[R/plots-barcodes.R:10:26:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L10) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        name <- names(bcb$barcodes[a])\n                         ^\n```\n[R/plots-barcodes.R:11:27:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L11) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        sample_name <- bcb$metadata[name, \"sample_name\"]\n                          ^\n```\n[R/plots-barcodes.R:13:19:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L13) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        bcs <- bcb$barcodes[a] %>%\n                  ^\n```\n[R/plots-barcodes.R:17:45:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L17) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​            mutate(log10_reads = log10(.data$reads))\n                                            ^\n```\n[R/plots-barcodes.R:18:29:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L18) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        bcs_hist <- hist(bcs$log10_reads, plot = FALSE, n = 50)\n                            ^\n```\n[R/plots-barcodes.R:18:63:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L18) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        bcs_hist <- hist(bcs$log10_reads, plot = FALSE, n = 50)\n                                                            ~~^\n```\n[R/plots-barcodes.R:19:9:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L19) *style:* **Variable or function name should be snake_case.**\n```r\n​        fLog <- bcs_hist$count\n        ^~~~\n```\n[R/plots-barcodes.R:19:25:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L19) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        fLog <- bcs_hist$count\n                        ^\n```\n[R/plots-barcodes.R:20:9:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L20) *style:* **Variable or function name should be snake_case.**\n```r\n​        xLog <- bcs_hist$mids\n        ^~~~\n```\n[R/plots-barcodes.R:20:25:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L20) *warning:* **Use `[[` instead of `$`  to extract an element.**\n```r\n​        xLog <- bcs_hist$mids\n                        ^\n```\n[R/plots-barcodes.R:21:24:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L21) *style:* **Put spaces around all infix operators.**\n```r\n​        y <- fLog * (10^xLog) / sum(fLog * (10^xLog))\n                      ~^~\n```\n[R/plots-barcodes.R:21:24:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L21) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        y <- fLog * (10^xLog) / sum(fLog * (10^xLog))\n                     ~~^\n```\n[R/plots-barcodes.R:21:47:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L21) *style:* **Put spaces around all infix operators.**\n```r\n​        y <- fLog * (10^xLog) / sum(fLog * (10^xLog))\n                                             ~^~\n```\n[R/plots-barcodes.R:21:47:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L21) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        y <- fLog * (10^xLog) / sum(fLog * (10^xLog))\n                                            ~~^\n```\n[R/plots-barcodes.R:22:17:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L22) *style:* **Put spaces around all infix operators.**\n```r\n​        qplot(10^xLog, y) +\n               ~^~\n```\n[R/plots-barcodes.R:22:17:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L22) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​        qplot(10^xLog, y) +\n              ~~^\n```\n[R/plots-barcodes.R:27:62:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L27) *style:* **Put spaces around all infix operators.**\n```r\n​                breaks = trans_breaks(\"log10\", function(x) 10^x),\n                                                            ~^~\n```\n[R/plots-barcodes.R:27:62:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L27) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​                breaks = trans_breaks(\"log10\", function(x) 10^x),\n                                                           ~~^\n```\n[R/plots-barcodes.R:28:63:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L28) *style:* **Put spaces around all infix operators.**\n```r\n​                labels = trans_format(\"log10\", math_format(~10^.x))) +\n                                                             ~^~\n```\n[R/plots-barcodes.R:28:63:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L28) *style:* **Integers should not be implicit. Use the form 1L for integers or 1.0 for doubles.**\n```r\n​                labels = trans_format(\"log10\", math_format(~10^.x))) +\n                                                            ~~^\n```\n[R/plots-barcodes.R:36:17:](https://github.com/hbc/bcbioSinglecell/blob/d63611240f3f14be2bdcb174c505fee725c6e793/R/plots-barcodes.R#L36) *warning:* **no visible global function definition for 'unlist_barcodes'**\n```r\n​    barcodes <- unlist_barcodes(bcb)\n                ^~~~~~~~~~~~~~~\n```"}}
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