comparison ez_histograms.R @ 1:fbedb212982d draft default tip

planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms commit 5e25392164eca5585239b62c82b7f6ba326cda6e

0:bdf40b0924cb

library(ggplot2)
library(reshape2)
library(dplyr)
library(scales)
library(vtable)
library(optparse)

options(show.error.messages = FALSE,
  error = function() {
    cat(geterrmessage(), file = stderr())

  } 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

)
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)

1:fbedb212982d

library(ggplot2)
library(reshape2)
library(dplyr)
library(scales)
library(psych)
library(optparse)

options(show.error.messages = FALSE,
  error = function() {
    cat(geterrmessage(), file = stderr())

  } else {
    return(FALSE)
  }
}

##### prepare input data

data <- read.delim(file = opt$file, header = test_header(opt$file))
data <- data %>% select(where(is.numeric))  # remove non numeric columns
mdata <- melt(data)

##### main

)
pdf(opt$pdf, width = width, height = height)
print(p + facet_wrap(~variable, ncol = ncol, scales = "free"))
dev.off()

# Summary statistics with psych package
summary_df <- describe(x = data, skew = FALSE, ranges = FALSE, quant = c(.25, .50, .75))
summary_df <- cbind(var_names = rownames(summary_df), summary_df)
colnames(summary_df)[2] <- "var_num"
summary_df <- summary_df[, -6]
summary_df[, 4:8] <- format(summary_df[, 4:8], scientific = TRUE)
write.table(summary_df, file = opt$summary, sep = "\t", quote = FALSE, row.names = FALSE)