Reading and writing ‘GraphPad Prism’ files in R

Yue Jiang

2022-08-21

Source: vignettes/pzfx.Rmd

Background

GraphPad Prism is a software application for scientific graphing, curve fitting and statistical testing. It has been popular among scientists, especially experimental biologists. The pzfx R package provides an easy way to read data tables that are in GraphPad Prism format (.pzfx files) into R and vise versa. Since Prism5 (the current version as of mid 2018 is Prism7), Prism stores its data tables in XML format and is possible to be parsed in R. The pzfx package manipulates GraphPad Prism XML files through functions provided by xml2.

Main functionality

Reading

There are two main functions for reading. pzfx_tables lists the tables in a .pzfx file. read_pzfx reads one table into R from a .pzfx file.

We use a Prism example file exponential_decay.pzfx to show how these two functions work. Here is the screen shot of this file when opened in Prism. data

List tables from a .pzfx file:

library(pzfx)
pzfx_tables(system.file("extdata/exponential_decay.pzfx", package="pzfx"))
#> [1] "Exponential decay"

Read one specific table into R by table name:

df <- read_pzfx(system.file("extdata/exponential_decay.pzfx", package="pzfx"), table="Exponential decay")
head(df)
#>   Minutes Control_1 Control_2 Control_3 Treated_1 Treated_2 Treated_3
#> 1       1      8887      7366      9612      6532      7905      7907
#> 2       2      8329        NA      8850      5352      5841      6277
#> 3       3      7907      8810      8669      5177      4082      3157
#> 4       4      7413      8481      6489      3608        NA      4226
#> 5       5      7081      7178      5716      2559      3697      2816
#> 6       6      6249      6492        NA      1671      3053      2891

Read one specific table into R by table index (1-based):

df <- read_pzfx(system.file("extdata/exponential_decay.pzfx", package="pzfx"), table=1)
head(df)
#>   Minutes Control_1 Control_2 Control_3 Treated_1 Treated_2 Treated_3
#> 1       1      8887      7366      9612      6532      7905      7907
#> 2       2      8329        NA      8850      5352      5841      6277
#> 3       3      7907      8810      8669      5177      4082      3157
#> 4       4      7413      8481      6489      3608        NA      4226
#> 5       5      7081      7178      5716      2559      3697      2816
#> 6       6      6249      6492        NA      1671      3053      2891

Writing

There is a write_pzfx function for writing. It takes as input a data frame or a matrix, or a named list of data frames or matrices, and writes to a .pzfx file. To keep row names and use them as row titles in .pzfx, specify argument row_names=TRUE. To specify a column (column 1, “Col1” for example) to be used as the “X” column, specify argument x_col=1 or x_col="Col1".

tmp <- tempfile(fileext=".pzfx")
write_pzfx(df, tmp, row_names=FALSE, x_col="Minutes")
out_df <- read_pzfx(tmp, table=1)
head(out_df)
#>   Minutes Control_1 Control_2 Control_3 Treated_1 Treated_2 Treated_3
#> 1       1      8887      7366      9612      6532      7905      7907
#> 2       2      8329        NA      8850      5352      5841      6277
#> 3       3      7907      8810      8669      5177      4082      3157
#> 4       4      7413      8481      6489      3608        NA      4226
#> 5       5      7081      7178      5716      2559      3697      2816
#> 6       6      6249      6492        NA      1671      3053      2891
unlink(tmp)

Additional notes

  • Prism allows subcolumns. To accommodate this, read_pzfx automatically adds _1, _2 etc to the original column name to account for sub columns if they represent replicates. It tries to infer the subcolumn types and adds appropriate suffix accordingly. For example, trailing _MEAN, _SD, _N are added if subcolumns represent mean, standard deviation and number of observations.

  • Prism does not require columns in a table to be of the same length. To accommodate this, NAs are added if the columns are of different lengths.

  • Prism allows user to exclude data by striking them out individual observations. To accommodate this, an option strike_action is available in read_pzfx. One can choose to delete these values with strike_action="exclude", keep them with "keep", or convert them to a trailing “*” (as they appear in Prism) with "star". Note if strike_action="star" the entire table is converted to type character.

  • Prism allows special formating of column names such as superscripts. When reading into R, column names with special formating are converted to regular strings.

  • For writing, because R data frames and matrices don’t support hierachical columns, the written out .pzfx files can only be of type “Column” or “XY”, depending on whether the “X” column is specified by x_col.