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Fix errors in plot functions. Also update DESCRIPTION file. #50

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merged 3 commits into from
Jun 22, 2024
Merged

Fix errors in plot functions. Also update DESCRIPTION file. #50

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c65299a
Fix error in plot function of comparePCASubspace, and update appearan…
AnthonyChristidis Jun 22, 2024
c243e9c
Add ORCID to DESCRIPTION file.
AnthonyChristidis Jun 22, 2024
28debf9
Merge pull request #8 from ccb-hms/main
AnthonyChristidis Jun 22, 2024
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,8 @@ Title: Cell type annotation diagnostics
Version: 0.99.0
Authors@R: c(
person("Anthony", "Christidis", role = c("aut", "cre"),
email = "anthony-alexander_christidis@hms.harvard.edu"),
email = "anthony-alexander_christidis@hms.harvard.edu",
comment = c(ORCID = "0000-0002-4565-6279")),
person("Andrew", "Ghazi", role = "aut"),
person("Smriti", "Chawla", role = "aut"),
person("Nitesh", "Turaga", role = "ctb"),
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8 changes: 5 additions & 3 deletions R/plot.compareCCA.R
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Expand Up @@ -39,8 +39,10 @@ plot.compareCCA <- function(x, ...){
x = "",
y = "Cosine Similarity of CC Coefficients",
size = "Correlation") +
ggplot2::theme_minimal() +
ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1,
size = 12, hjust = 1))
ggplot2::theme_bw() +
ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1, size = 12, hjust = 1),
axis.title = ggplot2::element_text(size = 12), axis.text = ggplot2::element_text(size = 10),
panel.grid.minor = ggplot2::element_blank(),
panel.grid.major = ggplot2::element_line(color = "gray", linetype = "dotted"))
return(cca_plot)
}
18 changes: 10 additions & 8 deletions R/plot.comparePCASubspace.R
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Expand Up @@ -26,11 +26,11 @@
plot.comparePCASubspace <- function(x, ...){

# Create a data frame for plotting
x <- data.frame(PC = paste0("Ref PC", x$cosine_id[, 1],
" - Query PC", x$cosine_id[, 2]),
Cosine = x$cosine_similarity,
VarianceExplained = subspace_comparison$var_explained_avg)
x$PC <- factor(x$PC, levels = x$PC)
x <- data.frame(PC = paste0("Ref PC", x[["cosine_id"]][, 1],
" - Query PC", x[["cosine_id"]][, 2]),
Cosine = x[["cosine_similarity"]],
VarianceExplained = x[["var_explained_avg"]])
x[["PC"]] <- factor(x[["PC"]], levels = x[["PC"]])

# Create plot
pc_plot <- ggplot2::ggplot(x, ggplot2::aes(x = PC, y = Cosine, size = VarianceExplained)) +
Expand All @@ -40,8 +40,10 @@ plot.comparePCASubspace <- function(x, ...){
x = "",
y = "Cosine Similarity of Principal Angle",
size = "Variance Explained") +
ggplot2::theme_minimal() +
ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1,
size = 12, hjust = 1))
ggplot2::theme_bw() +
ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1, size = 12, hjust = 1),
axis.title = ggplot2::element_text(size = 12), axis.text = ggplot2::element_text(size = 10),
panel.grid.minor = ggplot2::element_blank(),
panel.grid.major = ggplot2::element_line(color = "gray", linetype = "dotted"))
return(pc_plot)
}
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