From a0781fccd5f2928cec6932448af22800c1ca0f89 Mon Sep 17 00:00:00 2001 From: jbengler Date: Fri, 8 Dec 2023 22:36:12 +0100 Subject: [PATCH] Initial commit --- NAMESPACE | 1 + R/adjust.R | 14 + R/data.R | 4 +- R/todo.R | 8 - _pkgdown.yml | 3 +- data-raw/gene_expression.R | 10 + data-raw/gene_expression.csv | 1602 ++++++++--------- data-raw/{disease_course.R => time_course.R} | 19 +- ...idy_disease_course.txt => time_course.txt} | 0 data/disease_course.rda | Bin 1541 -> 0 bytes data/gene_expression.rda | Bin 8171 -> 9867 bytes data/time_course.rda | Bin 0 -> 1552 bytes man/adjust_padding.Rd | 31 + man/figures/README-example-1.png | Bin 54635 -> 54930 bytes man/{disease_course.Rd => time_course.Rd} | 10 +- 15 files changed, 876 insertions(+), 826 deletions(-) rename data-raw/{disease_course.R => time_course.R} (71%) rename data-raw/{tidy_disease_course.txt => time_course.txt} (100%) delete mode 100644 data/disease_course.rda create mode 100644 data/time_course.rda create mode 100644 man/adjust_padding.Rd rename man/{disease_course.Rd => time_course.Rd} (68%) diff --git a/NAMESPACE b/NAMESPACE index 14abce6a..ae336f5c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -63,6 +63,7 @@ export(adjust_flip) export(adjust_fontsize) export(adjust_labels) export(adjust_legend) +export(adjust_padding) export(adjust_size) export(adjust_x_axis) export(adjust_y_axis) diff --git a/R/adjust.R b/R/adjust.R index 6b42d8d9..c380c493 100644 --- a/R/adjust.R +++ b/R/adjust.R @@ -326,6 +326,20 @@ adjust_legend <- function(gg, title = ggplot2::waiver(), position = "right") { ggplot2::theme(legend.position = position) } +#' Adjust padding +#' @param gg bla +#' @param top bla +#' @param right bla +#' @param bottom bla +#' @param left bla +#' @param force_y_continuous bla +#' @export +adjust_padding <- function(gg, top = NULL, right = NULL, bottom = NULL, left = NULL, force_y_continuous = FALSE) { + gg %>% + adjust_x_axis(padding_left = left, padding_right = right) %>% + adjust_y_axis(padding_bottom = bottom, padding_top = top, force_y_continuous = force_y_continuous) +} + #' Flip plot #' @param gg bla #' @param ... bla diff --git a/R/data.R b/R/data.R index ffa3cecd..68afafa1 100644 --- a/R/data.R +++ b/R/data.R @@ -12,11 +12,11 @@ #' `tidyplots` package "gene_statistics" -#' Disease course data +#' Time course data #' @format A data frame with 800 rows and 9 variables. #' @source #' `tidyplots` package -"disease_course" +"time_course" #' Energy data #' @format A data frame with 242 rows and 4 variables. diff --git a/R/todo.R b/R/todo.R index d8cbefe9..4743d35e 100644 --- a/R/todo.R +++ b/R/todo.R @@ -1,12 +1,4 @@ -# heatmap have no color legend - -# adjust_padding(tlbr) - -# data set "de_analysis" for volcano plots - -# data set "disease_course" for plotting - # work on check_pipeline() # enforce "sequence of funs", with warnings and errors diff --git a/_pkgdown.yml b/_pkgdown.yml index 43f116b2..843f2a19 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -68,6 +68,7 @@ reference: - starts_with("adjust_size") - starts_with("adjust_fontsize") - starts_with("adjust_legend") + - starts_with("adjust_padding") - starts_with("adjust_flip") - starts_with("adjust_annotation") - title: Themes @@ -99,4 +100,4 @@ reference: - starts_with("study") - gene_expression - gene_statistics - - disease_course + - time_course diff --git a/data-raw/gene_expression.R b/data-raw/gene_expression.R index 5e75effd..0a263665 100644 --- a/data-raw/gene_expression.R +++ b/data-raw/gene_expression.R @@ -5,3 +5,13 @@ library(tidyverse) gene_expression <- read_csv(file = "data-raw/gene_expression.csv") usethis::use_data(gene_expression, overwrite = TRUE) + +library(tidyplots) +library(tidyverse) + +gene_expression %>% + tidyplot(sample, external_gene_name, color = expression, width = 100) %>% + add_heatmap(scale = "row") %>% + adjust_labels(var = external_gene_name, sort_by = -padj) %>% + adjust_labels(var = direction, reverse = TRUE)+ + facet_wrap(vars(direction), scales = "free") diff --git a/data-raw/gene_expression.csv b/data-raw/gene_expression.csv index 3d33ea82..3eb75321 100644 --- a/data-raw/gene_expression.csv +++ b/data-raw/gene_expression.csv @@ -1,801 +1,801 @@ -ensembl_gene_id,external_gene_name,sample,expression,group,sample_type,condition,is_immune_gene,direction -ENSMUSG00000033576,Apol6,Hin_1,2.2037551036479623,Hin,input,healthy,no,up -ENSMUSG00000033576,Apol6,Hin_2,2.2037551036479623,Hin,input,healthy,no,up -ENSMUSG00000033576,Apol6,Hin_3,2.660557981274521,Hin,input,healthy,no,up -ENSMUSG00000033576,Apol6,Hin_4,2.6495337084191877,Hin,input,healthy,no,up -ENSMUSG00000033576,Apol6,Hin_5,3.442740432961632,Hin,input,healthy,no,up -ENSMUSG00000033576,Apol6,Ein_1,5.030997477349095,Ein,input,EAE,no,up -ENSMUSG00000033576,Apol6,Ein_2,5.31441184724134,Ein,input,EAE,no,up -ENSMUSG00000033576,Apol6,Ein_3,5.372403375368066,Ein,input,EAE,no,up -ENSMUSG00000033576,Apol6,Ein_4,5.536959985338722,Ein,input,EAE,no,up 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-ENSMUSG00000014602,Kif1a,Eip_5,14.38519158231564,Eip,IP,EAE,no,up -ENSMUSG00000027254,Map1a,Hin_1,13.417763721992086,Hin,input,healthy,yes,up -ENSMUSG00000027254,Map1a,Hin_2,13.772931840771284,Hin,input,healthy,yes,up -ENSMUSG00000027254,Map1a,Hin_3,13.446421581944376,Hin,input,healthy,yes,up -ENSMUSG00000027254,Map1a,Hin_4,13.530706120391995,Hin,input,healthy,yes,up -ENSMUSG00000027254,Map1a,Hin_5,13.201874612177557,Hin,input,healthy,yes,up -ENSMUSG00000027254,Map1a,Ein_1,13.563317671021645,Ein,input,EAE,yes,up -ENSMUSG00000027254,Map1a,Ein_2,13.414517815989491,Ein,input,EAE,yes,up -ENSMUSG00000027254,Map1a,Ein_3,13.374582097290352,Ein,input,EAE,yes,up -ENSMUSG00000027254,Map1a,Ein_4,13.211265400544704,Ein,input,EAE,yes,up -ENSMUSG00000027254,Map1a,Ein_5,13.125640394148155,Ein,input,EAE,yes,up -ENSMUSG00000027254,Map1a,Hip_1,13.819813187138383,Hip,IP,healthy,yes,up -ENSMUSG00000027254,Map1a,Hip_2,13.550660062630987,Hip,IP,healthy,yes,up -ENSMUSG00000027254,Map1a,Hip_3,13.495390650146913,Hip,IP,healthy,yes,up -ENSMUSG00000027254,Map1a,Hip_4,12.977464624050501,Hip,IP,healthy,yes,up -ENSMUSG00000027254,Map1a,Hip_5,12.929211962068395,Hip,IP,healthy,yes,up -ENSMUSG00000027254,Map1a,Eip_1,14.300342433036729,Eip,IP,EAE,yes,up -ENSMUSG00000027254,Map1a,Eip_2,14.931126195205378,Eip,IP,EAE,yes,up -ENSMUSG00000027254,Map1a,Eip_3,14.920672917368575,Eip,IP,EAE,yes,up -ENSMUSG00000027254,Map1a,Eip_4,14.732255385142071,Eip,IP,EAE,yes,up -ENSMUSG00000027254,Map1a,Eip_5,15.269623164527362,Eip,IP,EAE,yes,up -ENSMUSG00000104453,Gm37829,Hin_1,3.911792228960392,Hin,input,healthy,no,up -ENSMUSG00000104453,Gm37829,Hin_2,4.704230454171995,Hin,input,healthy,no,up -ENSMUSG00000104453,Gm37829,Hin_3,4.474479548459191,Hin,input,healthy,no,up -ENSMUSG00000104453,Gm37829,Hin_4,3.7962586116765378,Hin,input,healthy,no,up -ENSMUSG00000104453,Gm37829,Hin_5,4.124559774166667,Hin,input,healthy,no,up -ENSMUSG00000104453,Gm37829,Ein_1,4.462019590764584,Ein,input,EAE,no,up -ENSMUSG00000104453,Gm37829,Ein_2,4.90911305937105,Ein,input,EAE,no,up -ENSMUSG00000104453,Gm37829,Ein_3,4.627397595143855,Ein,input,EAE,no,up -ENSMUSG00000104453,Gm37829,Ein_4,4.31621381463161,Ein,input,EAE,no,up -ENSMUSG00000104453,Gm37829,Ein_5,3.7110948880107357,Ein,input,EAE,no,up -ENSMUSG00000104453,Gm37829,Hip_1,2.2037551036479623,Hip,IP,healthy,no,up -ENSMUSG00000104453,Gm37829,Hip_2,2.2037551036479623,Hip,IP,healthy,no,up -ENSMUSG00000104453,Gm37829,Hip_3,2.2037551036479623,Hip,IP,healthy,no,up -ENSMUSG00000104453,Gm37829,Hip_4,2.2037551036479623,Hip,IP,healthy,no,up -ENSMUSG00000104453,Gm37829,Hip_5,2.2037551036479623,Hip,IP,healthy,no,up -ENSMUSG00000104453,Gm37829,Eip_1,9.246378462497201,Eip,IP,EAE,no,up -ENSMUSG00000104453,Gm37829,Eip_2,2.2037551036479623,Eip,IP,EAE,no,up -ENSMUSG00000104453,Gm37829,Eip_3,7.156942055903421,Eip,IP,EAE,no,up -ENSMUSG00000104453,Gm37829,Eip_4,2.2037551036479623,Eip,IP,EAE,no,up -ENSMUSG00000104453,Gm37829,Eip_5,2.2037551036479623,Eip,IP,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Hin_1,8.827457919319977,Hin,input,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hin_2,8.456041722991529,Hin,input,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hin_3,8.726761156069227,Hin,input,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hin_4,8.808307580969073,Hin,input,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hin_5,8.656032137081928,Hin,input,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Ein_1,8.639146424113793,Ein,input,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Ein_2,8.861327274340077,Ein,input,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Ein_3,8.84987322175448,Ein,input,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Ein_4,9.273811132018386,Ein,input,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Ein_5,9.404787635069882,Ein,input,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Hip_1,8.5286715857569,Hip,IP,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hip_2,8.086715313495882,Hip,IP,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hip_3,9.274335740000692,Hip,IP,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hip_4,7.894408144172189,Hip,IP,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Hip_5,9.084301167054155,Hip,IP,healthy,no,up -ENSMUSG00000042492,Tbc1d10b,Eip_1,10.594684948469258,Eip,IP,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Eip_2,11.215602953879038,Eip,IP,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Eip_3,10.784057043321814,Eip,IP,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Eip_4,11.092944178661604,Eip,IP,EAE,no,up -ENSMUSG00000042492,Tbc1d10b,Eip_5,9.72854383554715,Eip,IP,EAE,no,up -ENSMUSG00000031879,Fam96b,Hin_1,7.835156960918539,Hin,input,healthy,no,down -ENSMUSG00000031879,Fam96b,Hin_2,7.517774049494821,Hin,input,healthy,no,down -ENSMUSG00000031879,Fam96b,Hin_3,7.957167130195198,Hin,input,healthy,no,down -ENSMUSG00000031879,Fam96b,Hin_4,8.045902977266277,Hin,input,healthy,no,down -ENSMUSG00000031879,Fam96b,Hin_5,8.081315081890844,Hin,input,healthy,no,down -ENSMUSG00000031879,Fam96b,Ein_1,7.3019718847995,Ein,input,EAE,no,down -ENSMUSG00000031879,Fam96b,Ein_2,6.356636138896669,Ein,input,EAE,no,down -ENSMUSG00000031879,Fam96b,Ein_3,7.066704557729076,Ein,input,EAE,no,down -ENSMUSG00000031879,Fam96b,Ein_4,6.68915535364021,Ein,input,EAE,no,down -ENSMUSG00000031879,Fam96b,Ein_5,7.317450099967253,Ein,input,EAE,no,down -ENSMUSG00000031879,Fam96b,Hip_1,8.756578131121271,Hip,IP,healthy,no,down -ENSMUSG00000031879,Fam96b,Hip_2,9.641596461364504,Hip,IP,healthy,no,down -ENSMUSG00000031879,Fam96b,Hip_3,9.161601886874534,Hip,IP,healthy,no,down -ENSMUSG00000031879,Fam96b,Hip_4,9.031910668921093,Hip,IP,healthy,no,down -ENSMUSG00000031879,Fam96b,Hip_5,8.66704556575816,Hip,IP,healthy,no,down -ENSMUSG00000031879,Fam96b,Eip_1,5.036368865646446,Eip,IP,EAE,no,down -ENSMUSG00000031879,Fam96b,Eip_2,2.2037551036479623,Eip,IP,EAE,no,down -ENSMUSG00000031879,Fam96b,Eip_3,5.396466897264531,Eip,IP,EAE,no,down -ENSMUSG00000031879,Fam96b,Eip_4,6.7654385767755185,Eip,IP,EAE,no,down -ENSMUSG00000031879,Fam96b,Eip_5,6.373782497697378,Eip,IP,EAE,no,down -ENSMUSG00000058267,Mrps14,Hin_1,9.088216431996555,Hin,input,healthy,no,down -ENSMUSG00000058267,Mrps14,Hin_2,8.681237945762842,Hin,input,healthy,no,down -ENSMUSG00000058267,Mrps14,Hin_3,8.922262030343273,Hin,input,healthy,no,down -ENSMUSG00000058267,Mrps14,Hin_4,8.876584006462865,Hin,input,healthy,no,down -ENSMUSG00000058267,Mrps14,Hin_5,9.258165983320612,Hin,input,healthy,no,down -ENSMUSG00000058267,Mrps14,Ein_1,8.500837484308063,Ein,input,EAE,no,down -ENSMUSG00000058267,Mrps14,Ein_2,7.942846831335884,Ein,input,EAE,no,down -ENSMUSG00000058267,Mrps14,Ein_3,8.427252576899253,Ein,input,EAE,no,down -ENSMUSG00000058267,Mrps14,Ein_4,8.188273810504997,Ein,input,EAE,no,down -ENSMUSG00000058267,Mrps14,Ein_5,8.342834578206373,Ein,input,EAE,no,down -ENSMUSG00000058267,Mrps14,Hip_1,9.832043074908446,Hip,IP,healthy,no,down -ENSMUSG00000058267,Mrps14,Hip_2,10.285114080220389,Hip,IP,healthy,no,down -ENSMUSG00000058267,Mrps14,Hip_3,10.44613926587321,Hip,IP,healthy,no,down -ENSMUSG00000058267,Mrps14,Hip_4,10.01723783681495,Hip,IP,healthy,no,down -ENSMUSG00000058267,Mrps14,Hip_5,11.68190280897734,Hip,IP,healthy,no,down -ENSMUSG00000058267,Mrps14,Eip_1,7.6273006034113715,Eip,IP,EAE,no,down -ENSMUSG00000058267,Mrps14,Eip_2,8.184125884451795,Eip,IP,EAE,no,down -ENSMUSG00000058267,Mrps14,Eip_3,8.491744940744832,Eip,IP,EAE,no,down -ENSMUSG00000058267,Mrps14,Eip_4,7.70501297011035,Eip,IP,EAE,no,down -ENSMUSG00000058267,Mrps14,Eip_5,7.481523924892258,Eip,IP,EAE,no,down -ENSMUSG00000091537,Tma7,Hin_1,6.81123902617366,Hin,input,healthy,no,down -ENSMUSG00000091537,Tma7,Hin_2,6.566973539272292,Hin,input,healthy,no,down -ENSMUSG00000091537,Tma7,Hin_3,6.949656343434403,Hin,input,healthy,no,down -ENSMUSG00000091537,Tma7,Hin_4,6.908018603901578,Hin,input,healthy,no,down -ENSMUSG00000091537,Tma7,Hin_5,7.116899725154566,Hin,input,healthy,no,down -ENSMUSG00000091537,Tma7,Ein_1,6.844332724875409,Ein,input,EAE,no,down -ENSMUSG00000091537,Tma7,Ein_2,7.254254780243957,Ein,input,EAE,no,down -ENSMUSG00000091537,Tma7,Ein_3,7.016477790998231,Ein,input,EAE,no,down -ENSMUSG00000091537,Tma7,Ein_4,6.784851409010417,Ein,input,EAE,no,down -ENSMUSG00000091537,Tma7,Ein_5,7.150363444149281,Ein,input,EAE,no,down -ENSMUSG00000091537,Tma7,Hip_1,8.193744620351834,Hip,IP,healthy,no,down -ENSMUSG00000091537,Tma7,Hip_2,8.906014804666794,Hip,IP,healthy,no,down -ENSMUSG00000091537,Tma7,Hip_3,9.061287535605258,Hip,IP,healthy,no,down -ENSMUSG00000091537,Tma7,Hip_4,8.231773954425904,Hip,IP,healthy,no,down -ENSMUSG00000091537,Tma7,Hip_5,9.12036029252888,Hip,IP,healthy,no,down -ENSMUSG00000091537,Tma7,Eip_1,6.303793963655521,Eip,IP,EAE,no,down -ENSMUSG00000091537,Tma7,Eip_2,5.908812749261368,Eip,IP,EAE,no,down -ENSMUSG00000091537,Tma7,Eip_3,5.188813475492764,Eip,IP,EAE,no,down -ENSMUSG00000091537,Tma7,Eip_4,6.1036970636324455,Eip,IP,EAE,no,down -ENSMUSG00000091537,Tma7,Eip_5,7.052701632671625,Eip,IP,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Hin_1,7.09906929700469,Hin,input,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hin_2,6.641979832727378,Hin,input,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hin_3,7.059649976645307,Hin,input,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hin_4,7.361730585220356,Hin,input,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hin_5,7.0935854698410825,Hin,input,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Ein_1,6.844332724875409,Ein,input,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Ein_2,5.794391319668565,Ein,input,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Ein_3,6.338816433840995,Ein,input,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Ein_4,5.536959985338722,Ein,input,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Ein_5,6.228243715256553,Ein,input,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Hip_1,8.030265038845242,Hip,IP,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hip_2,8.767909617262477,Hip,IP,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hip_3,9.211132721738412,Hip,IP,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hip_4,8.529566640186562,Hip,IP,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Hip_5,9.025541309142126,Hip,IP,healthy,no,down -ENSMUSG00000021951,Eef1akmt1,Eip_1,6.593406626840181,Eip,IP,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Eip_2,4.392885532672507,Eip,IP,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Eip_3,6.345959509292537,Eip,IP,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Eip_4,5.605475371210288,Eip,IP,EAE,no,down -ENSMUSG00000021951,Eef1akmt1,Eip_5,5.145524570097416,Eip,IP,EAE,no,down -ENSMUSG00000057469,E2f6,Hin_1,8.896741192719007,Hin,input,healthy,no,down -ENSMUSG00000057469,E2f6,Hin_2,9.150440056440626,Hin,input,healthy,no,down -ENSMUSG00000057469,E2f6,Hin_3,8.964572913760096,Hin,input,healthy,no,down 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+ENSMUSG00000036553,Sh3tc1,Hin_2,3.945668953815874,Hin,input,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hin_3,3.721780782425808,Hin,input,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hin_4,4.071979261455928,Hin,input,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hin_5,3.5693613399508783,Hin,input,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Ein_1,5.758297712891266,Ein,input,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Ein_2,5.628463970942804,Ein,input,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Ein_3,4.943715492835961,Ein,input,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Ein_4,5.004403443263173,Ein,input,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Ein_5,5.505736748151263,Ein,input,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hip_1,2.2037551036479623,Hip,IP,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hip_2,2.2037551036479623,Hip,IP,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hip_3,2.2037551036479623,Hip,IP,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hip_4,2.9324468885364987,Hip,IP,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Hip_5,2.2037551036479623,Hip,IP,healthy,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Eip_1,8.434457369878807,Eip,IP,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Eip_2,8.051110907260599,Eip,IP,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Eip_3,3.7192670659896905,Eip,IP,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Eip_4,5.605475371210288,Eip,IP,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000036553,Sh3tc1,Eip_5,7.439714469782121,Eip,IP,EAE,no,up,7.89440662423533,1.54271136555115e-19 +ENSMUSG00000032589,Bsn,Hin_1,9.59469241229078,Hin,input,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hin_2,9.481154748607096,Hin,input,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hin_3,9.663026999610224,Hin,input,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hin_4,9.621491884009597,Hin,input,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hin_5,9.25488923513046,Hin,input,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Ein_1,9.549501407372556,Ein,input,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Ein_2,10.336688349455562,Ein,input,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Ein_3,9.978071972164708,Ein,input,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Ein_4,9.82380052946352,Ein,input,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Ein_5,9.465945893775933,Ein,input,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hip_1,9.427565544413046,Hip,IP,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hip_2,9.40176862050274,Hip,IP,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hip_3,9.52087740070882,Hip,IP,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hip_4,9.264846851942076,Hip,IP,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Hip_5,10.194224986763173,Hip,IP,healthy,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Eip_1,11.871814281861578,Eip,IP,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Eip_2,11.444949719144894,Eip,IP,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Eip_3,11.08334622553713,Eip,IP,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Eip_4,11.58509261814276,Eip,IP,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000032589,Bsn,Eip_5,11.489940765438025,Eip,IP,EAE,no,up,1.91778941801284,1.13567002501193e-16 +ENSMUSG00000034936,Arl4d,Hin_1,6.379306238102802,Hin,input,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hin_2,5.795141145477338,Hin,input,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hin_3,5.767257979792665,Hin,input,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hin_4,5.991696348135113,Hin,input,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hin_5,6.256381271782062,Hin,input,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Ein_1,5.5136012488307315,Ein,input,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Ein_2,5.697177813400821,Ein,input,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Ein_3,6.555628820944611,Ein,input,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Ein_4,6.031177507520569,Ein,input,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Ein_5,7.073764442860339,Ein,input,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hip_1,4.493476025635952,Hip,IP,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hip_2,4.561037728722876,Hip,IP,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hip_3,4.20544763651574,Hip,IP,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hip_4,4.4382806129919725,Hip,IP,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Hip_5,4.835291362535578,Hip,IP,healthy,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Eip_1,6.55248096714547,Eip,IP,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Eip_2,7.099168714426773,Eip,IP,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Eip_3,6.695912071276458,Eip,IP,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Eip_4,8.63763904665001,Eip,IP,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000034936,Arl4d,Eip_5,8.449851662373874,Eip,IP,EAE,no,up,3.72147494757494,1.7195356896732202e-15 +ENSMUSG00000037428,Vgf,Hin_1,7.386505383465285,Hin,input,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hin_2,6.861793586948436,Hin,input,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hin_3,7.2660030145657375,Hin,input,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hin_4,7.738055444642946,Hin,input,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hin_5,7.575900858009973,Hin,input,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Ein_1,7.385140219723912,Ein,input,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Ein_2,7.39435060461406,Ein,input,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Ein_3,7.393357728030717,Ein,input,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Ein_4,7.676218716055792,Ein,input,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Ein_5,7.781865326377871,Ein,input,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hip_1,9.049623942248592,Hip,IP,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hip_2,9.300448910484954,Hip,IP,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hip_3,9.204563345157716,Hip,IP,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hip_4,8.585648684773838,Hip,IP,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Hip_5,9.51459685589406,Hip,IP,healthy,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Eip_1,10.931662159995383,Eip,IP,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Eip_2,11.184190657189852,Eip,IP,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Eip_3,11.17653635099507,Eip,IP,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Eip_4,10.864962852791,Eip,IP,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000037428,Vgf,Eip_5,12.16034415138021,Eip,IP,EAE,no,up,2.19010912347962,3.5257180760193203e-15 +ENSMUSG00000017670,Elmo2,Hin_1,8.964593886898875,Hin,input,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hin_2,9.191505476721415,Hin,input,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hin_3,8.996498053124554,Hin,input,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hin_4,9.091160673638392,Hin,input,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hin_5,8.877599293630213,Hin,input,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Ein_1,8.940427685138289,Ein,input,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Ein_2,8.777252865072908,Ein,input,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Ein_3,8.986456653042012,Ein,input,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Ein_4,8.935157870326703,Ein,input,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Ein_5,9.130373247907588,Ein,input,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hip_1,9.052208901096591,Hip,IP,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hip_2,8.822091651258335,Hip,IP,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hip_3,8.525198319741472,Hip,IP,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hip_4,9.101037502401551,Hip,IP,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Hip_5,8.908268354417032,Hip,IP,healthy,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Eip_1,9.97074749016054,Eip,IP,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Eip_2,10.031207690487658,Eip,IP,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Eip_3,9.857982307774936,Eip,IP,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Eip_4,9.872046436111628,Eip,IP,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000017670,Elmo2,Eip_5,10.027213755003777,Eip,IP,EAE,no,up,1.07234973123913,8.639471442968591e-15 +ENSMUSG00000048065,Cyb5r2,Hin_1,3.8461359061556433,Hin,input,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hin_2,4.181117258960689,Hin,input,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hin_3,3.778345648523412,Hin,input,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hin_4,3.6878232874730017,Hin,input,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hin_5,3.817429825975408,Hin,input,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Ein_1,4.242324326846366,Ein,input,EAE,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Ein_2,4.330927663936197,Ein,input,EAE,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Ein_3,3.9066548720810497,Ein,input,EAE,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Ein_4,4.122089151673591,Ein,input,EAE,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Ein_5,4.180508214033256,Ein,input,EAE,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hip_1,2.2037551036479623,Hip,IP,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hip_2,2.2037551036479623,Hip,IP,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hip_3,2.2037551036479623,Hip,IP,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hip_4,2.2037551036479623,Hip,IP,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Hip_5,2.2037551036479623,Hip,IP,healthy,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Eip_1,6.728107177242672,Eip,IP,EAE,no,up,8.33468211785826,3.61552446327932e-14 +ENSMUSG00000048065,Cyb5r2,Eip_2,2.2037551036479623,Eip,IP,EAE,no,up,8.33468211785826,3.61552446327932e-14 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rename to data-raw/time_course.R index 1c14f4fe..de8bda67 100644 --- a/data-raw/disease_course.R +++ b/data-raw/time_course.R @@ -1,29 +1,30 @@ -## code to prepare `disease_course` dataset goes here +## code to prepare `time_course` dataset goes here library(tidyverse) -disease_course <- - read_tsv("data-raw/tidy_disease_course.txt") +time_course <- + read_tsv("data-raw/time_course.txt") -usethis::use_data(disease_course, overwrite = TRUE) +usethis::use_data(time_course, overwrite = TRUE) -library(tidyplots) - -disease_course %>% +time_course %>% tidyplot(x = day, y = score, color = treatment, dodge_width = 0) %>% add_mean_line() %>% add_mean_dot() %>% add_error_ribbon() -disease_course %>% +library(tidyverse) + +time_course %>% tidyplot(x = day, y = subject, color = score, height = 80) %>% add_heatmap(rotate_labels = FALSE) + facet_grid(vars(treatment), scales = "free") -disease_course %>% +time_course %>% tidyplot(x = day, y = subject, color = score, height = 80) %>% 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+\alias{adjust_padding} +\title{Adjust padding} +\usage{ +adjust_padding( + gg, + top = NULL, + right = NULL, + bottom = NULL, + left = NULL, + force_y_continuous = FALSE +) +} +\arguments{ +\item{gg}{bla} + +\item{top}{bla} + +\item{right}{bla} + +\item{bottom}{bla} + +\item{left}{bla} + +\item{force_y_continuous}{bla} +} +\description{ +Adjust padding +} diff --git a/man/figures/README-example-1.png b/man/figures/README-example-1.png index 3d4ff0aac4694389f480c490c491ca5d65711969..5041b649a8995bd3e08a127fcf9ac07fca309a92 100644 GIT binary patch literal 54930 zcmeFZWmJ^w8$K!sTfsmDL_q;XL>g2;L0}A|B%~V!iJ`lO0mnvCkd8s6Te?9dq&tU_ zuAv)dIM0h)!0q1a{6C#_&N{yjuJsDM&-=uk*L~fOo2<0xF;Z&M0|yQq6BoNDci;eV z&w&GkGl%~IKgpzTeQ@9a(Q)|QyRyc2MemxMm|MwPJl53{)icwxg6qnO-Z^mKhNq{Z zrr|k73Zc-v4Ax8a&s$?+e2?RK-e;P~HNEH_$LnR7_OSVxWZw3vn(hsUU%oc96$NJ& zqPTtHOWc6pz_$7qrVB=iSaZ&?SF&qR>T zr8fk>yZT03gzZX#2fhsR=Fk|!iW<=&>p6_qEuOe!=8H8VRlJEI(hMy{&o^DOMS6|P 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-1,9 +1,9 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/data.R \docType{data} -\name{disease_course} -\alias{disease_course} -\title{Disease course data} +\name{time_course} +\alias{time_course} +\title{Time course data} \format{ A data frame with 800 rows and 9 variables. } @@ -11,9 +11,9 @@ A data frame with 800 rows and 9 variables. \code{tidyplots} package } \usage{ -disease_course +time_course } \description{ -Disease course data +Time course data } \keyword{datasets}