Last updated: 2025-04-18

Checks: 6 1

Knit directory: CX5461_Project/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20250129)

The command set.seed(20250129) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

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File paths: relative

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Repository version: 3f37123

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The results in this page were generated with repository version 3f37123. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .RData
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    0.1 box.svg
    Ignored:    Rplot04.svg

Untracked files:
    Untracked:  0.1 density.svg
    Untracked:  0.1.emf
    Untracked:  0.1.svg
    Untracked:  0.5 box.svg
    Untracked:  0.5 density.svg
    Untracked:  0.5.svg
    Untracked:  CX_5461_Pattern_Genes_24hr.csv
    Untracked:  CX_5461_Pattern_Genes_3hr.csv
    Untracked:  DRC1.svg
    Untracked:  Figure 1.jpeg
    Untracked:  Figure 1.pdf
    Untracked:  Rplot.svg
    Untracked:  Rplot01.svg
    Untracked:  Rplot02.svg
    Untracked:  Rplot03.svg
    Untracked:  Rplot05.svg
    Untracked:  Rplot06.svg
    Untracked:  Rplot07.svg
    Untracked:  Rplot08.jpeg
    Untracked:  Rplot08.svg
    Untracked:  Rplot09.svg
    Untracked:  Rplot10.svg
    Untracked:  analysis/Flow.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

📌 iPSC-CM Purity analysis

# Load libraries
library(ggplot2)

# Data
purity_data <- data.frame(
  Individual = factor(c("Ind 1", "Ind 2", "Ind 3", "Ind 4", "Ind 5", "Ind 6"),
                      levels = c("Ind 1", "Ind 2", "Ind 3", "Ind 4", "Ind 5", "Ind 6")),
  Purity = c(99.7, 99.1, 98.6, 98.0, 98.1, 96.0)
)

# Colors matching your original figure
bar_colors <- c("#FDBE02", "#F50670", "#FB5403", "#933BEB", "#3E97FD", "#3A3F52")

# Plot
ggplot(purity_data, aes(x = Individual, y = Purity, fill = Individual)) +
  geom_bar(stat = "identity", width = 0.8, color = "black") +
  scale_fill_manual(values = bar_colors) +
  labs(title = "Cardiomyocyte Purity (Flow Cytometry)",
       x = "Individual", y = "CM Purity (%)") +
  theme_minimal(base_family = "Arial") +
  theme(
    plot.title = element_text(size = 18, face = "bold", hjust = 0.5),
    axis.title.x = element_text(size = 14, face = "bold"),
    axis.title.y = element_text(size = 14, face = "bold"),
    axis.text = element_text(size = 12),
    legend.position = "none",
    panel.grid.major = element_line(color = "gray70", size = 0.5),
    panel.grid.minor = element_blank(),
    panel.border = element_rect(color = "black", fill = NA, size = 1.2),
    axis.line = element_blank()
  ) +
  ylim(0, 105)
Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
not found in Windows font database
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
not found in Windows font database
Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family not found in Windows font database


sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.5.2

loaded via a namespace (and not attached):
 [1] gtable_0.3.6      jsonlite_2.0.0    crayon_1.5.3      dplyr_1.1.4      
 [5] compiler_4.3.0    promises_1.3.2    tidyselect_1.2.1  Rcpp_1.0.12      
 [9] stringr_1.5.1     git2r_0.36.2      later_1.3.2       jquerylib_0.1.4  
[13] scales_1.3.0      yaml_2.3.10       fastmap_1.2.0     R6_2.6.1         
[17] labeling_0.4.3    generics_0.1.3    workflowr_1.7.1   knitr_1.50       
[21] tibble_3.2.1      munsell_0.5.1     rprojroot_2.0.4   bslib_0.9.0      
[25] pillar_1.10.2     rlang_1.1.3       cachem_1.1.0      stringi_1.8.3    
[29] httpuv_1.6.15     xfun_0.52         fs_1.6.3          sass_0.4.10      
[33] cli_3.6.1         withr_3.0.2       magrittr_2.0.3    digest_0.6.34    
[37] grid_4.3.0        rstudioapi_0.17.1 lifecycle_1.0.4   vctrs_0.6.5      
[41] evaluate_1.0.3    glue_1.7.0        farver_2.1.2      colorspace_2.1-0 
[45] rmarkdown_2.29    tools_4.3.0       pkgconfig_2.0.3   htmltools_0.5.8.1