| Next changeset 1:fbedb212982d (2024-02-08) |
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Commit message:
planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 443759a746f78d67dc4ffcafdc6610d09d278846 |
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added:
ez_histograms.R ez_histograms.xml test-data/classic.pdf test-data/classic.tsv test-data/count.pdf test-data/counts.tsv test-data/headless.pdf test-data/headless.tsv test-data/large.pdf test-data/large.tsv test-data/rowheadless.pdf test-data/rowheadless.tsv test-data/single_headed_col.pdf test-data/single_headed_col.tsv test-data/summary_1.tsv test-data/summary_2.tsv test-data/summary_3.tsv test-data/summary_4.tsv test-data/summary_5.tsv test-data/summary_6.tsv |
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| diff -r 000000000000 -r bdf40b0924cb ez_histograms.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ez_histograms.R Wed Feb 07 19:49:56 2024 +0000 |
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| @@ -0,0 +1,169 @@ +library(ggplot2) +library(reshape2) +library(dplyr) +library(scales) +library(vtable) +library(optparse) + +options(show.error.messages = FALSE, + error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE) + } +) + +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +warnings() + +option_list <- list( + make_option( + c("-f", "--file"), + default = NA, + type = "character", + help = "Input file that contains count values to transform" + ), + make_option( + c("-d", "--profile"), + default = "count", + type = "character", + help = "Whether y-axis shows absolute counts or density: 'count' or 'density' [default : '%default' ]" + ), + make_option( + "--xscale", + default = "cartesian", + type = "character", + help = "Whether x-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]" + ), + make_option( + "--yscale", + default = "cartesian", + type = "character", + help = "Whether y-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]" + ), + make_option( + c("-p", "--pdf"), + default = "histograms.pdf", + type = "character", + help = "Output pdf file name [default : '%default' ]" + ), + make_option( + c("-s", "--summary"), + default = "summary.tsv", + type = "character", + help = "statistics summary file name [default : '%default' ]" + ) +) + +opt <- parse_args(OptionParser(option_list = option_list), + args = commandArgs(trailingOnly = TRUE)) + +plot_histograms <- function(mdata, profile = "count", xscale = "cartesian", yscale = "cartesian", bins = 30) { + if (profile == "count") { + # count histogram + p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) + + geom_histogram(bins = bins) + theme(legend.position = "none") + if (xscale == "cartesian") { + if (yscale == "log2") { + p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x))) + } else { + if (yscale == "log10") { + p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x))) + } + } + } + if (xscale == "log2") { + p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x))) + if (yscale == "log2") { + p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x))) + } else { + if (yscale == "log10") { + p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x))) + } + } + } + if (xscale == "log10") { + p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x))) + if (yscale == "log2") { + p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x))) + } else { + if (yscale == "log10") { + p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x))) + } + } + } + } + + if (profile == "density") { + # density histogram + p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) + + geom_density() + theme(legend.position = "none") + if (xscale == "log2") { + p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x))) + } + if (xscale == "log10") { + p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x))) + } + } + return(p) +} + +test_header <- function(file) { + data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2) + if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) { + return(TRUE) + } else { + return(FALSE) + } +} + +test_rownames <- function(file) { + data <- read.delim(file = file, header = FALSE, row.names = NULL, nrows = 2) + if (is.na(as.numeric(data[2, 1]))) { + return(1) + } else { + return(NULL) + } +} + +##### prepare input data +data <- read.delim(file = opt$file, header = test_header(opt$file), row.names = test_rownames(opt$file)) +data <- data %>% select(where(is.numeric)) # remove non numeric columns +mdata <- melt(data) + +##### main + +# determine optimal number of bins (Sturges’ Rule) +bins <- ceiling(log2(nrow(data)) + 1) +# plot +p <- plot_histograms(mdata, profile = opt$profile, xscale = opt$xscale, bins = bins, yscale = opt$yscale) + +# determine optimal width for the graph +width <- length(data) +width <- case_when( + width == 1 ~ 14 / 3, + width == 2 ~ (2 / 3) * 14, + TRUE ~ 14 +) +# determine optimal height for the graph +height <- length(data) +height <- case_when( + height <= 3 ~ 3, + height <= 6 ~ 6, + TRUE ~ (floor(height / 3) + 1) * 3 +) +# determine optimal number of col for the graph +ncol <- length(data) +ncol <- case_when( + ncol == 1 ~ 1, + ncol == 2 ~ 2, + TRUE ~ 3 +) +pdf(opt$pdf, width = width, height = height) +print(p + facet_wrap(~variable, ncol = ncol, scales = "free")) +dev.off() + +# Summary statistics with vtable package +summary_df <- sumtable(data, digits = 8, out = "return", add.median = TRUE, + summ.names = c("N", "Mean", "Std. Dev.", "Min", "Pctl. 25", + "Median", "Pctl. 75", "Max")) +write.table(summary_df, file = opt$summary, sep = "\t", quote = FALSE, row.names = FALSE) |
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| diff -r 000000000000 -r bdf40b0924cb ez_histograms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ez_histograms.xml Wed Feb 07 19:49:56 2024 +0000 |
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| @@ -0,0 +1,166 @@ +<tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <macros> + <token name="@TOOL_VERSION@">3.4.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + </macros> + <requirements> + <requirement type="package" version="3.4.4">r-ggplot2</requirement> + <requirement type="package" version="1.4.4">r-reshape2</requirement> + <requirement type="package" version="1.1.4">r-dplyr</requirement> + <requirement type="package" version="1.3.0">r-scales</requirement> + <requirement type="package" version="1.4.6">r-vtable</requirement> + <requirement type="package" version="1.7.4">r-optparse</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/ez_histograms.R + --file '$file' + --profile '$plot_options.plot_options_selector' + --xscale '$plot_options.xscale' + #if str($plot_options.plot_options_selector) == "count": + --yscale '$plot_options.yscale' + #end if + --pdf '$pdf' + --summary '$summary' + ]]></command> + + <inputs> + <param name="file" type="data" format="tabular" label="Input tabular dataset" + help="Only numeric columns will be plotted"/> + <conditional name="plot_options"> + <param name="plot_options_selector" type="select" label="Set plot types"> + <option value="count" selected="true">Count Histograms</option> + <option value="density">Density Plots</option> + </param> + <when value="density"> + <param name="xscale" type="select" label="Set x-axis scale"> + <option value="cartesian" selected="true">Cartesian</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> + </when> + <when value="count"> + <param name="xscale" type="select" label="Set x-axis scale"> + <option value="cartesian" selected="true">Cartesian</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> + <param name="yscale" type="select" label="Set y-axis scale"> + <option value="cartesian" selected="true">Cartesian</option> + <option value="log2">log2</option> + <option value="log10">log10</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="pdf" format="pdf" label="${tool.name} plots from ${on_string}"/> + <data name="summary" format="tabular" label="Statistics Summary from ${on_string}"/> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="file" value="classic.tsv"/> + <param name="plot_options_selector" value="count"/> + <param name="xscale" value="cartesian"/> + <param name="yscale" value="cartesian"/> + <output name="pdf" file="classic.pdf"/> + <output name="summary" file="summary_1.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="counts.tsv"/> + <param name="plot_options_selector" value="count"/> + <param name="xscale" value="log2"/> + <param name="yscale" value="cartesian"/> + <output name="pdf" file="count.pdf"/> + <output name="summary" file="summary_2.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="headless.tsv"/> + <param name="plot_options_selector" value="count"/> + <param name="xscale" value="log10"/> + <param name="yscale" value="log2"/> + <output name="pdf" file="headless.pdf"/> + <output name="summary" file="summary_3.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="large.tsv"/> + <param name="plot_options_selector" value="density"/> + <param name="xscale" value="log2"/> + <output name="pdf" file="large.pdf"/> + <output name="summary" file="summary_4.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="rowheadless.tsv"/> + <param name="plot_options_selector" value="density"/> + <param name="xscale" value="cartesian"/> + <output name="pdf" file="rowheadless.pdf"/> + <output name="summary" file="summary_5.tsv"/> + </test> + <test expect_num_outputs="2"> + <param name="file" value="single_headed_col.tsv"/> + <param name="plot_options_selector" value="density"/> + <param name="xscale" value="log10"/> + <output name="pdf" file="single_headed_col.pdf"/> + <output name="summary" file="summary_6.tsv"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +The tool generates faceted histograms or density plots using the ggplot2 functions +geom_histogram() or geom_density(), respectively. + +**Inputs** + +Any regular tabular data, provided that the number of columns (tabulations) is unchanged +for any row. + +Except for the first one, any column will be considered as one variable with n_rows +observations. However, non-numeric columns will be filtered and will not be considered +variables. + +If the first column is not numeric, it will be taken as row names (ie observation identifiers), +otherwise, it will be considered as the first numerical variable of the table. + +If the first row is not numerical, it will be considered as a header, ie as describing the +variable names. + +If you provide a table without header, variable names will be assigned to each column +following the R default rule: (V1), V2, ..., Vn + +**Parameters** + +For Count Histograms, both x- and y-axis can have linear (cartesian), log2 or log10 scales. + +For Density Plots, only x-axis can be customized with linear (cartesian), log2, or log10 +scales + +**Outputs** + +The ez_histograms Galaxy tool returns + +- A pdf file with plots faceted on three columns +- A tsv file with statistics summary of the variables generated by the R package vtables + + ]]></help> + <citations> + <citation type="bibtex"> +@BOOK{Wickham2016-ic, + title = "Ggplot2: Elegant graphics for data analysis", + author = "Wickham, Hadley", + publisher = "Springer International Publishing", + series = "Use R!", + edition = 2, + month = jun, + year = 2016, + address = "Cham, Switzerland", + language = "en", + isbn = "9783319242774" +} </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r bdf40b0924cb test-data/classic.pdf |
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| Binary file test-data/classic.pdf has changed |
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| diff -r 000000000000 -r bdf40b0924cb test-data/classic.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/classic.tsv Wed Feb 07 19:49:56 2024 +0000 |
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| diff -r 000000000000 -r bdf40b0924cb test-data/headless.pdf |
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| Binary file test-data/headless.pdf has changed |
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| diff -r 000000000000 -r bdf40b0924cb test-data/headless.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/headless.tsv Wed Feb 07 19:49:56 2024 +0000 |
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| diff -r 000000000000 -r bdf40b0924cb test-data/large.pdf |
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| diff -r 000000000000 -r bdf40b0924cb test-data/large.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/large.tsv Wed Feb 07 19:49:56 2024 +0000 |
| b |
| b'@@ -0,0 +1,1001 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|
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/rowheadless.pdf |
| b |
| Binary file test-data/rowheadless.pdf has changed |
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/rowheadless.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rowheadless.tsv Wed Feb 07 19:49:56 2024 +0000 |
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|
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/summary_1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_1.tsv Wed Feb 07 19:49:56 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max +BaseMean 990 1091.5132 2625.4763 0 31.199603 249.39264 1054.0101 33915.214 +log2FC 849 -0.38999858 1.9953097 -5.2835189 -2.0088992 -0.86544745 1.2737699 5.6079286 +StdErr 849 0.30667747 0.1285766 0.089282127 0.1962894 0.28928034 0.39630761 0.56482292 +Wald.Stats 849 -0.95820431 6.3140778 -21.603869 -5.9077253 -4.475739 5.2726083 19.585597 +P.value 848 0.030010804 0.15185376 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016518389 0.0000000000036649168 0.000000012325875 0.0000022785953 0.98727107 +P.adj 813 0.00004223522 0.000078050135 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000034761298 0.000000000255376 0.00000044934286 0.000034873651 0.00028949939 |
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/summary_2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_2.tsv Wed Feb 07 19:49:56 2024 +0000 |
| b |
| @@ -0,0 +1,16 @@ +Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max +GCB_Mg_S2 1000 672.224 1727.7831 0 69 236.5 700 38072 +GCB_Mg_S7 1000 830.225 1848.5916 0 91.5 317 857.25 34261 +GCB_Mg_S12 1000 685.564 1662.1423 0 71 253 686.25 33558 +GCB_S1 1000 450.654 1224.5977 0 38 152 459.5 29464 +GCB_S6 1000 547.793 1344.4334 0 51 194 550 28567 +GCB_S11 1000 481.844 1310.3546 0 40 152.5 462.5 29614 +GW_S5 1000 698.673 1534.1178 0 63.75 237.5 697.75 26119 +GW_S10 1000 573.137 1477.6949 0 49.75 176.5 504 29920 +GW_S15 1000 718.612 1730.7819 0 69 233.5 676 33878 +NS_S4 1000 824.02 1624.4871 0 100 336 914 28284 +NS_S9 1000 704.673 1266.9907 0 93.5 305 796.25 21678 +NS_S14 1000 883.989 1636.9581 0 114.75 366.5 1016 25492 +Starch_S3 1000 905.783 1464.8208 1 135.75 430 1099 22970 +Starch_S8 1000 973.323 1680.7842 0 138.75 426.5 1092.75 24999 +Starch_S13 1000 752.171 1404.0569 0 93 310.5 846.25 22556 |
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/summary_3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_3.tsv Wed Feb 07 19:49:56 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max +V2 1000 1286.6999 2744.7392 6.5122425 100.50742 409.92217 1309.8068 33915.214 +V3 1000 -0.4092237 1.9730612 -5.2835189 -2.0884579 -0.946016 1.2600548 5.6079286 +V4 1000 0.30466439 0.1311528 0.089282127 0.19205135 0.28205562 0.40370597 0.56482292 +V5 1000 -0.9419943 6.2085133 -21.603869 -5.7808572 -4.5659907 5.0667272 19.585597 +V6 1000 0.0000018003049 0.000003260254 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016518389 0.00000000002981881 0.000000042451763 0.0000019035803 0.000013756861 +V7 1000 0.000042996682 0.00007258655 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000034761298 0.0000000025022835 0.000001784909 0.000053393931 0.00028949939 |
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/summary_4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_4.tsv Wed Feb 07 19:49:56 2024 +0000 |
| b |
| @@ -0,0 +1,97 @@ +Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max +SC_ph2_46_WT_d0 1000 3.11773 2.1477193 0 1.0975 3.285 4.7525 10.19 +SC_ph2_46_WT_d2 1000 3.63747 2.359001 0 1.525 3.935 5.33 12.17 +SC_ph2_46_WT_d4 1000 3.63669 2.4152548 0 1.2475 3.99 5.4 12.17 +SC_ph2_46_WT_d6 1000 3.66312 2.4765653 0 1.08 4.165 5.61 11.72 +SC_ph2_46_WT_d9 1000 3.73941 2.4700576 0 1.33 4.335 5.64 11.77 +SC_ph2_46_WT_d11 1000 3.61458 2.5333163 0 0.95 4.16 5.59 13.31 +SC_ph2_46_WT_d14 1000 3.64982 2.592493 0 0.715 4.14 5.6525 13.62 +SC_ph2_44_KO_d0 1000 3.76101 2.2973781 0 1.9975 4.065 5.46 11.42 +SC_ph2_44_KO_d2 1000 3.63091 2.39967 0 1.37 3.945 5.35 12.17 +SC_ph2_44_KO_d4 1000 3.74617 2.4163269 0 1.4925 4.105 5.52 12.37 +SC_ph2_44_KO_d6 1000 3.77324 2.3972206 0 1.67 4.245 5.5925 11.55 +SC_ph2_44_KO_d9 1000 3.79138 2.4189072 0 1.675 4.24 5.5925 11.58 +SC_ph2_44_KO_d11 1000 3.77987 2.4282298 0 1.715 4.29 5.58 12.36 +SC_ph2_44_KO_d14 1000 3.80486 2.4590689 0 1.44 4.345 5.63 12.76 +SC_ph2_42_WT_d0 1000 3.79097 2.3332375 0 2.0075 4.13 5.51 10.82 +SC_ph2_42_WT_d2 1000 3.61533 2.3936933 0 1.43 3.945 5.305 12.16 +SC_ph2_42_WT_d4 1000 3.66082 2.4648083 0 1.26 4.015 5.52 12.18 +SC_ph2_42_WT_d6 1000 3.70802 2.4459409 0 1.43 4.2 5.61 11.73 +SC_ph2_42_WT_d9 1000 3.78185 2.4286019 0 1.685 4.25 5.5925 11.73 +SC_ph2_42_WT_d11 1000 3.72851 2.5039993 0 1.2075 4.265 5.6625 12.96 +SC_ph2_42_WT_d14 1000 3.75931 2.5118435 0 1.17 4.255 5.62 13.31 +SC_ph2_20_KO_d0 1000 3.08787 2.117815 0 1.2375 3.22 4.64 9.94 +SC_ph2_20_KO_d4 1000 3.66303 2.4181179 0 1.31 4.08 5.39 12.04 +SC_ph2_20_KO_d6 1000 3.66579 2.4111765 0 1.3075 4.17 5.53 11.45 +SC_ph2_20_KO_d9 1000 3.73288 2.4179454 0 1.42 4.25 5.55 11.64 +SC_ph2_20_KO_d11 1000 3.60288 2.495575 0 0.8875 4.125 5.52 13.3 +SC_ph2_20_KO_d14 1000 3.5964 2.5132892 0 0.86 4.05 5.48 13.62 +SC_wtc11_62_WT_d0 1000 3.40212 2.2730132 0 1.3925 3.665 5.1025 9.86 +SC_wtc11_62_WT_d2 1000 3.63876 2.4205571 0 1.44 4.03 5.355 11.8 +SC_wtc11_62_WT_d4 1000 3.64659 2.4836605 0 1.1 4.035 5.4925 11.5 +SC_wtc11_62_WT_d6 1000 3.71569 2.4669429 0 1.4 4.26 5.6 11.35 +SC_wtc11_62_WT_d9 1000 3.80686 2.4744861 0 1.435 4.345 5.6825 11.63 +SC_wtc11_62_WT_d11 1000 3.59131 2.5337838 0 0.8875 4.05 5.525 13.35 +SC_wtc11_62_WT_d14 1000 3.7034 2.5457967 0 0.98 4.225 5.59 13.3 +SC_wtc11_59_WT_d0 1000 3.71923 2.303389 0 1.77 4.075 5.48 11.05 +SC_wtc11_59_WT_d2 1000 3.61826 2.405514 0 1.3875 3.98 5.355 11.73 +SC_wtc11_59_WT_d4 1000 3.64446 2.4750506 0 1.1675 4.04 5.53 12.04 +SC_wtc11_59_WT_d6 1000 3.73685 2.4738724 0 1.2275 4.285 5.6025 11.58 +SC_wtc11_59_WT_d9 1000 3.79347 2.4629366 0 1.425 4.325 5.64 11.71 +SC_wtc11_59_WT_d11 1000 3.8024 2.4913136 0 1.2275 4.38 5.66 12.97 +SC_wtc11_59_WT_d14 1000 3.74929 2.5130639 0 1.1875 4.195 5.615 13.63 +SC_wtc11_44_KO_d0 1000 3.75231 2.410491 0 1.615 4.09 5.5225 11.68 +SC_wtc11_44_KO_d2 1000 3.56306 2.4033411 0 1.2275 3.855 5.33 11.64 +SC_wtc11_44_KO_d4 1000 3.66319 2.457765 0 1.245 4.06 5.5125 11.92 +SC_wtc11_44_KO_d6 1000 3.73555 2.4341219 0 1.3875 4.215 5.5625 11.19 +SC_wtc11_44_KO_d9 1000 3.80402 2.4530618 0 1.44 4.32 5.6125 11.37 +SC_wtc11_44_KO_d11 1000 3.82832 2.4438198 0 1.635 4.355 5.61 12.4 +SC_wtc11_44_KO_d14 1000 3.77796 2.4686382 0 1.39 4.22 5.6125 13.43 +CBI_NG_5925_d0 1000 3.81391 2.314134 0 2.01 4.115 5.455 11.72 +CBI_NG_5925_d7 1000 3.88046 2.3760604 0 1.8975 4.235 5.605 12.15 +CBI_NG_5925_d14 1000 4.03084 2.3810075 0 2.115 4.485 5.8 12.11 +CBI_NG_5925_d21 1000 4.0982 2.3553707 0 2.2275 4.505 5.8525 12.4 +CBI_NG_5925_d28 1000 4.01713 2.3419343 0 2.15 4.47 5.73 12.81 +CBI_NG_5925_d35 1000 4.0037 2.3726751 0 2.095 4.365 5.7225 13 +CBI_NG_2266_d0 1000 3.66515 2.3917919 0 1.6 3.92 5.4825 12.1 +CBI_NG_2266_d7 1000 3.829 2.3604446 0 2 4.125 5.53 12.73 +CBI_NG_2266_d14 1000 3.99827 2.3516933 0 2.1175 4.42 5.69 12.27 +CBI_NG_2266_d21 1000 4.01182 2.3036996 0 2.3475 4.425 5.6825 12.1 +CBI_NG_2266_d28 1000 3.90413 2.3318045 0 1.94 4.295 5.57 12.27 +CBI_NG_2266_d35 1000 3.84252 2.3786142 0 1.7875 4.235 5.55 12.35 +CBI_ph2_44_KO_d0 1000 3.71693 2.3525121 0 1.7375 3.975 5.44 11.18 +CBI_ph2_44_KO_d7 1000 3.78661 2.289096 0 2.095 4.12 5.45 12.18 +CBI_ph2_44_KO_d14 1000 4.00159 2.3666751 0 2.1375 4.47 5.77 11.65 +CBI_ph2_44_KO_d21 1000 4.07712 2.3450134 0 2.3475 4.57 5.8 11.31 +CBI_ph2_44_KO_d28 1000 3.91843 2.3934397 0 2.0175 4.375 5.67 11.92 +CBI_ph2_44_KO_d35 1000 3.87058 2.415086 0 1.8675 4.3 5.59 11.56 +CBI_ph2_25_WT_d0 1000 3.67504 2.3151791 0 1.7075 3.885 5.3925 11.42 +CBI_ph2_25_WT_d7 1000 3.76218 2.2711381 0 2.0075 4.155 5.4325 12.05 +CBI_ph2_25_WT_d14 1000 3.93884 2.3528151 0 2.065 4.405 5.71 12.34 +CBI_ph2_25_WT_d21 1000 4.09695 2.3071569 0 2.51 4.55 5.7775 12.68 +CBI_ph2_25_WT_d28 1000 3.98384 2.2701825 0 2.2675 4.435 5.64 12.17 +CBI_ph2_25_WT_d35 1000 3.95099 2.2635005 0 2.3775 4.34 5.56 12.27 +CBII_NG_5925_d7 1000 3.83078 2.3576249 0 1.8975 4.195 5.5325 12.12 +CBII_NG_5925_d14 1000 3.98798 2.3425078 0 2.095 4.44 5.75 12.3 +CBII_NG_5925_d21 1000 4.09168 2.2692616 0 2.44 4.54 5.77 12.56 +CBII_NG_5925_d28 1000 4.12182 2.2650885 0 2.5975 4.545 5.7725 12.89 +CBII_NG_5925_d35 1000 4.06331 2.2135581 0 2.59 4.46 5.5725 12.97 +CBII_NG_2266_d7 1000 3.64617 2.2955894 0 1.7825 3.95 5.335 12.34 +CBII_NG_2266_d14 1000 3.92017 2.3435342 0 1.985 4.38 5.65 11.98 +CBII_NG_2266_d21 1000 3.93792 2.2685917 0 2.32 4.325 5.59 11.76 +CBII_NG_2266_d28 1000 3.92191 2.3337922 0 2.08 4.345 5.5825 11.41 +CBII_NG_2266_d35 1000 3.77144 2.3628802 0 1.7825 4.215 5.4625 11.75 +CBII_ph2_44_KO_d7 1000 3.79221 2.3017856 0 1.9175 4.165 5.48 12.27 +CBII_ph2_44_KO_d14 1000 3.94071 2.3415082 0 2.11 4.455 5.6825 11.21 +CBII_ph2_44_KO_d21 1000 3.95096 2.3618465 0 2.145 4.44 5.6925 11.2 +CBII_ph2_44_KO_d28 1000 3.92924 2.447976 0 1.915 4.375 5.71 11.65 +CBII_ph2_44_KO_d35 1000 3.90667 2.4296602 0 1.825 4.35 5.65 11.96 +CBII_ph2_25_WT_d7 1000 3.83587 2.3139054 0 2.0125 4.24 5.55 12.12 +CBII_ph2_25_WT_d14 1000 3.924 2.3734098 0 1.985 4.42 5.6725 12.55 +CBII_ph2_25_WT_d21 1000 4.00121 2.2999763 0 2.3225 4.46 5.68 12.87 +CBII_ph2_25_WT_d28 1000 4.08491 2.3131296 0 2.405 4.585 5.81 12.44 +CBII_ph2_25_WT_d35 1000 3.99314 2.2755044 0 2.3025 4.415 5.62 12.45 +CBIII_ph2_25_WT_d14 1000 3.84399 2.3219652 0 1.895 4.29 5.5625 12.19 +CBIII_ph2_25_WT_d21 1000 3.94112 2.288597 0 2.1575 4.38 5.61 12.84 +CBIII_ph2_25_WT_d28 1000 4.02923 2.2982489 0 2.35 4.53 5.6825 12.62 +CBIII_ph2_25_WT_d35 1000 3.98047 2.2670942 0 2.3175 4.44 5.6775 12.19 |
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/summary_5.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_5.tsv Wed Feb 07 19:49:56 2024 +0000 |
| b |
| @@ -0,0 +1,7 @@ +Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max +V1 1000 1286.6999 2744.7392 6.5122425 100.50742 409.92217 1309.8068 33915.214 +V2 1000 -0.4092237 1.9730612 -5.2835189 -2.0884579 -0.946016 1.2600548 5.6079286 +V3 1000 0.30466439 0.1311528 0.089282127 0.19205135 0.28205562 0.40370597 0.56482292 +V4 1000 -0.9419943 6.2085133 -21.603869 -5.7808572 -4.5659907 5.0667272 19.585597 +V5 1000 0.0000018003049 0.000003260254 0.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000016518389 0.00000000002981881 0.000000042451763 0.0000019035803 0.000013756861 +V6 1000 0.000042996682 0.00007258655 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000034761298 0.0000000025022835 0.000001784909 0.000053393931 0.00028949939 |
| b |
| diff -r 000000000000 -r bdf40b0924cb test-data/summary_6.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_6.tsv Wed Feb 07 19:49:56 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Variable N Mean Std. Dev. Min Pctl. 25 Median Pctl. 75 Max +Counts 32833 630.15844 4127.3013 0 0 25 445 552918 |