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fix(dataProcessPlotsPTM, groupComparisonPlotsPTM): Migrate away from deprecated functions for ggplot #120

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Merged
tonywu1999 merged 4 commits into from
Sep 19, 2025
Merged

fix(dataProcessPlotsPTM, groupComparisonPlotsPTM): Migrate away from deprecated functions for ggplot #120

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9a67d57
replace aes_string with aes for dataProcessPlotsPTM
tonywu1999 Sep 18, 2025
1cdebcd
migrate aes_string to aes for group comparison plots
tonywu1999 Sep 18, 2025
1c2aa9d
migrate from size to linewidth msstatsptm
tonywu1999 Sep 18, 2025
b85cd80
migrate size to linewidth group comparison plots
tonywu1999 Sep 18, 2025
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86 changes: 43 additions & 43 deletions R/utils_dataProcessPlots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -293,12 +293,12 @@

yaxis.name = 'Log2-intensities'
## 1st plot for Protein plot
protein_temp = ggplot(aes_string(x = 'xorder', y = 'ABUNDANCE',
color = 'PSM', linetype = 'PSM'),
protein_temp = ggplot(aes(x = .data$xorder, y = .data$ABUNDANCE,
color = .data$PSM, linetype = .data$PSM),
data = sub) +
facet_grid(~RUN) +
geom_point(data = sub, aes(shape=CENSORED), size=dot.size.profile, na.rm=TRUE) +
geom_line(size = 0.5, na.rm=TRUE) +
geom_point(data = sub, aes(shape=.data$CENSORED), size=dot.size.profile, na.rm=TRUE) +
geom_line(linewidth = 0.5, na.rm=TRUE) +
scale_colour_manual(values=cbp[s]) +
scale_linetype_manual(values = ss) +
scale_shape_manual(values = c(16, 1),labels = c("Detected data", "Censored missing data")) +
Expand All @@ -307,10 +307,10 @@
scale_y_continuous(yaxis.name, limits = c(y.limdown, y.limup)) +
scale_x_continuous('MS runs') +
geom_vline(data = groupline.tmp,
aes(xintercept = cumGroupAxis),
aes(xintercept = .data$cumGroupAxis),
colour = "grey", linetype = "longdash") +
geom_text(data = groupline.all.tmp,
aes(x = xorder, y = abundance, label = CONDITION),
aes(x = .data$xorder, y = .data$abundance, label = .data$CONDITION),
size = text.size,
angle = text.angle, hjust = .9,
color = "black") +
Expand Down Expand Up @@ -418,13 +418,13 @@
yaxis.name = 'Log2-intensities'

## Draw summarized ptm plot
ptempall = ggplot(aes_string(x = 'xorder', y = 'ABUNDANCE',
color = 'analysis', linetype = 'PSM',
size = 'analysis'), data = final) +
ptempall = ggplot(aes(x = .data$xorder, y = .data$ABUNDANCE,
color = .data$analysis, linetype = .data$PSM,
size = .data$analysis), data = final) +
facet_grid(~RUN) +
# geom_point(size = dot.size.profile, na.rm=TRUE) +
geom_point(data = final, aes(shape=CENSORED), size=dot.size.profile, na.rm=TRUE) +
geom_line(size = 0.5, na.rm=TRUE) +
geom_point(data = final, aes(shape=.data$CENSORED), size=dot.size.profile, na.rm=TRUE) +
geom_line(linewidth = 0.5, na.rm=TRUE) +
scale_colour_manual(values = c("lightgray", "darkred")) +
scale_shape_manual(values = c(16, 1),labels = c("Detected data", "Censored missing data")) +
scale_size_manual(values = c(1.7, 2), guide = "none") +
Expand All @@ -434,10 +434,10 @@
x = 'MS runs') +
scale_y_continuous(yaxis.name, limits = c(y.limdown, y.limup)) +
geom_vline(data = groupline.tmp,
aes(xintercept = cumGroupAxis),
aes(xintercept = .data$cumGroupAxis),
colour = "grey", linetype = "longdash") +
geom_text(data = groupline.all.tmp,
aes(x = xorder, y = abundance, label = CONDITION),
aes(x = .data$xorder, y = .data$abundance, label = .data$CONDITION),
size = text.size,
angle = text.angle, hjust = .9,
color = "black") +
Expand All @@ -450,7 +450,7 @@

## draw point again because some red summary dots could be hiden
ptempall = ptempall + geom_point(data = final, aes(
x = xorder, y = ABUNDANCE, size = analysis, color = analysis)
x = .data$xorder, y = .data$ABUNDANCE, size = .data$analysis, color = .data$analysis)
)

return(ptempall)
Expand Down Expand Up @@ -717,18 +717,18 @@
## y-axis labeling
yaxis.name = 'Log2-intensities'

ptemp = ggplot(aes_string(x = 'xorder', y = 'ABUNDANCE'),
ptemp = ggplot(aes(x = .data$xorder, y = .data$ABUNDANCE),
data = datafeature) +
facet_grid(~RUN) +
geom_boxplot(aes_string(fill = 'CONDITION'), outlier.shape = 1,
geom_boxplot(aes(fill = .data$CONDITION), outlier.shape = 1,
outlier.size = 1.5) +
labs(title = title, x = 'MS runs') +
scale_y_continuous(yaxis.name, limits = c(ylimdown, ylimup)) +
geom_vline(data = groupline.tmp,
aes(xintercept = cumGroupAxis),
aes(xintercept = .data$cumGroupAxis),
colour = "grey", linetype = "longdash") +
geom_text(data = groupline.all.tmp,
aes(x = xorder, y = abundance, label = CONDITION),
aes(x = .data$xorder, y = .data$abundance, label = .data$CONDITION),
size = text.size,
angle = text.angle, hjust = .9,
color = "black") +
Expand Down Expand Up @@ -786,18 +786,18 @@
sub$xorder = factor(sub$xorder)
yaxis.name = 'Log2-intensities'

ptemp = ggplot(aes_string(x = 'xorder', y = 'ABUNDANCE'),
ptemp = ggplot(aes(x = .data$xorder, y = .data$ABUNDANCE),
data = sub) +
facet_grid(~RUN) +
geom_boxplot(aes_string(fill = 'CONDITION'), outlier.shape = 1,
geom_boxplot(aes(fill = .data$CONDITION), outlier.shape = 1,
outlier.size = 1.5) +
labs(title = protein, x = 'MS runs') +
scale_y_continuous(yaxis.name, limits = c(ylimdown, ylimup)) +
geom_vline(data = groupline.tmp,
aes(xintercept = cumGroupAxis),
aes(xintercept = .data$cumGroupAxis),
colour = "grey", linetype = "longdash") +
geom_text(data = groupline.all.tmp,
aes(x = xorder, y = abundance, label = CONDITION),
aes(x = .data$xorder, y = .data$abundance, label = .data$CONDITION),
size = text.size,
angle = text.angle, hjust = .9,
color = "black") +
Expand Down Expand Up @@ -1141,12 +1141,12 @@
sub$group_aes = paste(sub$CONDITION, sub$FEATURE, sep = "_")
## 1st plot for Protein plot
protein_temp = ggplot(data=sub) + facet_grid(~LABEL) +
geom_point(aes_string(x='RUN', y='ABUNDANCE',
color='FEATURE', shape='CENSORED'), #
geom_point(aes(x=.data$RUN, y=.data$ABUNDANCE,
color=.data$FEATURE, shape=.data$CENSORED), #
size=dot.size.profile, na.rm=TRUE) +
geom_line(aes_string(x='RUN', y='ABUNDANCE',
color='FEATURE', linetype='FEATURE'), #
size = 0.5, na.rm=TRUE) +
geom_line(aes(x=.data$RUN, y=.data$ABUNDANCE,
color=.data$FEATURE, linetype=.data$FEATURE), #
linewidth = 0.5, na.rm=TRUE) +
scale_colour_manual(values=cbp[s]) +
scale_linetype_manual(values = ss) +
scale_shape_manual(values = c(16, 1),labels = c("Detected data", "Censored missing data")) +
Expand All @@ -1155,10 +1155,10 @@
scale_y_continuous(yaxis.name, limits = c(y.limdown, y.limup)) +
scale_x_continuous('MS runs', breaks=groupNametemp$lineNameAxis) +
geom_vline(data = groupNametemp[lineNameAxis != 0],
aes(xintercept = lineNameAxis + 0.5),
aes(xintercept = .data$lineNameAxis + 0.5),
colour = "grey", linetype = "longdash") +
geom_text(data = groupNametemp,
aes_string(x = "RUN", y = "ABUNDANCE", label = "Name"),
aes(x = .data$RUN, y = .data$ABUNDANCE, label = .data$Name),
size = text.size,
angle = text.angle, hjust = .9,
color = "black") +
Expand Down Expand Up @@ -1247,10 +1247,10 @@

## Draw summarized ptm plot
ptempall = ggplot(data=final) +
geom_point(aes_string(x='RUN', y='ABUNDANCE',
color='analysis', shape='CENSORED'), size = dot.size.profile, na.rm=TRUE) +
geom_line(aes_string(x='RUN', y='ABUNDANCE',
color='analysis', linetype='FEATURE'), size = 0.5, na.rm=TRUE) +
geom_point(aes(x=.data$RUN, y=.data$ABUNDANCE,
color=.data$analysis, shape=.data$CENSORED), size = dot.size.profile, na.rm=TRUE) +
geom_line(aes(x=.data$RUN, y=.data$ABUNDANCE,
color=.data$analysis, linetype=.data$FEATURE), linewidth = 0.5, na.rm=TRUE) +
scale_colour_manual(values = c("lightgray", "darkred")) +
scale_shape_manual(values = c(16, 1),labels = c("Detected data", "Censored missing data")) +
scale_size_manual(values = c(1.7, 2), guide = "none") +
Expand All @@ -1260,10 +1260,10 @@
x = 'MS runs') +
scale_y_continuous(yaxis.name, limits = c(y.limdown, y.limup)) +
geom_vline(data = groupNametemp[lineNameAxis != 0],
aes(xintercept = lineNameAxis + 0.5),
aes(xintercept = .data$lineNameAxis + 0.5),
colour = "grey", linetype = "longdash") +
geom_text(data = groupNametemp,
aes(x = RUN, y = ABUNDANCE, label = Name),
aes(x = .data$RUN, y = .data$ABUNDANCE, label = .data$Name),
size = text.size,
angle = text.angle, hjust = .9,
color = "black") +
Expand Down Expand Up @@ -1528,17 +1528,17 @@
## y-axis labeling
yaxis.name = 'Log-intensities'

ptemp = ggplot(aes_string(x = 'RUN', y = 'ABUNDANCE'),
ptemp = ggplot(aes(x = .data$RUN, y = .data$ABUNDANCE),
data = datafeature) +
geom_boxplot(aes_string(fill = 'CONDITION'), outlier.shape = 1,
geom_boxplot(aes(fill = .data$CONDITION), outlier.shape = 1,
outlier.size = 1.5) +
labs(title = title, x = 'MS runs') +
scale_y_continuous(yaxis.name, y.limdown, y.limup) +
Comment on lines +1531 to 1536
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@coderabbitai coderabbitai bot Sep 18, 2025

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⚠️ Potential issue

QC (all, LF): fix limits arg and undefined text.angle

  • scale_y_continuous is using positional args; limits isn’t set.
  • text_angle = text.angle references an undefined symbol in this scope.

Apply:

-    scale_y_continuous(yaxis.name, y.limdown, y.limup) +
+    scale_y_continuous(yaxis.name, limits = c(y.limdown, y.limup)) +
@@
-    theme_msstats(type = "PROFILEPLOT", x.axis.size, y.axis.size,
-                  13, 
-                  element_rect(fill = "gray95"),
-                  element_text(colour = c("#00B0F6"), size = 14),
-                  "none", text_angle = text.angle)
+    theme_msstats(type = "PROFILEPLOT", x.axis.size, y.axis.size,
+                  13, 
+                  element_rect(fill = "gray95"),
+                  element_text(colour = c("#00B0F6"), size = 14),
+                  "none", text_angle = 0)

Also applies to: 1539-1542, 1549-1549

🤖 Prompt for AI Agents 
R/utils_dataProcessPlots.R lines ~1531-1536 (also apply same fixes at 1539-1542
and 1549): scale_y_continuous currently uses positional args so limits are not
set — change it to scale_y_continuous(limits = c(y.limdown, y.limup), name =
yaxis.name) to explicitly set limits and axis label; also replace the invalid
text_angle = text.angle usage with angle = text_angle (or use a defined variable
name consistently), ensuring text_angle is defined/passed into the function or
given a default so theme(element_text(angle = text_angle)) uses a valid symbol.

geom_vline(data = groupName.tmp[lineNameAxis != 0],
aes(xintercept = lineNameAxis + 0.5),
aes(xintercept = .data$lineNameAxis + 0.5),
colour = "grey", linetype = "longdash") +
geom_text(data = groupName.tmp,
aes(x = RUN, y = ABUNDANCE - 1, label = Name),
aes(x = .data$RUN, y = .data$ABUNDANCE - 1, label = .data$Name),
size = text.size,
angle = 0,color = "black") +
theme_msstats(type = "PROFILEPLOT", x.axis.size, y.axis.size,
Expand Down Expand Up @@ -1587,17 +1587,17 @@
## for boxplot, x-axis, xorder should be factor
yaxis.name = 'Log-intensities'

ptemp = ggplot(aes_string(x = 'RUN', y = 'ABUNDANCE'),
ptemp = ggplot(aes(x = .data$RUN, y = .data$ABUNDANCE),
data = sub) +
geom_boxplot(aes_string(fill = 'CONDITION'), outlier.shape = 1,
geom_boxplot(aes(fill = .data$CONDITION), outlier.shape = 1,
outlier.size = 1.5) +
labs(title = protein, x = 'MS runs') +
scale_y_continuous(yaxis.name, limits = c(y.limdown, y.limup)) +
geom_vline(data = groupname.tmp[lineNameAxis != 0],
Comment on lines +1590 to 1596
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⚠️ Potential issue

QC (single, LF): fix undefined text.angle

Same issue as above: text.angle isn’t defined in this function.

Apply:

-    theme_msstats(type = "PROFILEPLOT", x.axis.size, y.axis.size,
-                  13, 
-                  element_rect(fill = "gray95"),
-                  element_text(colour = c("#00B0F6"), size = 14),
-                  "none", text_angle = text.angle)
+    theme_msstats(type = "PROFILEPLOT", x.axis.size, y.axis.size,
+                  13, 
+                  element_rect(fill = "gray95"),
+                  element_text(colour = c("#00B0F6"), size = 14),
+                  "none", text_angle = 0)

Also applies to: 1598-1603

aes(xintercept = lineNameAxis + .5),
aes(xintercept = .data$lineNameAxis + .5),
colour = "grey", linetype = "longdash") +
geom_text(data = groupname.tmp,
aes(x = RUN, y = ABUNDANCE, label = Name),
aes(x = .data$RUN, y = .data$ABUNDANCE, label = .data$Name),
size = text.size,
color = "black") +
theme_msstats(type = "PROFILEPLOT", x.axis.size, y.axis.size,
Expand Down
28 changes: 14 additions & 14 deletions R/utils_groupComparisonPlots.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -302,7 +302,7 @@

limits = c(-1,1)*max(abs(temp_obj$sign_adj_pval[
is.finite(temp_obj$sign_adj_pval)]))
temp_heatmap = ggplot(temp_obj, aes(Label, Protein, fill = sign_adj_pval)
temp_heatmap = ggplot(temp_obj, aes(.data$Label, .data$Protein, fill = .data$sign_adj_pval)
) + geom_tile() + scale_fill_distiller(
palette = "RdBu", name = "(sign) Adj pvalue",
limits = limits) + labs(
Expand Down Expand Up @@ -528,9 +528,9 @@
log_title = 'Log10'
}

ptemp = ggplot(aes_string(x='logFC', y='logadjp',
color='colgroup',
label='Protein'),
ptemp = ggplot(aes(x = .data$logFC, y = .data$logadjp,
color = .data$colgroup,
label = .data$Protein),
data=subtemp) +
geom_point(size=dot.size) +
scale_colour_manual(values=c("gray65", "blue", "red"),
Expand All @@ -553,7 +553,7 @@
} else {
ptemp = ptemp +
geom_text_repel(data=subtemp[subtemp$colgroup != "black", ],
aes(label=Protein),
aes(label = .data$Protein),
size=text.size,
col='black')
}
Expand All @@ -579,9 +579,9 @@

pfinal = ptemp +
geom_line(data=sigcut,
aes_string(x='logFC', y='logadjp', linetype='line'),
aes(x = .data$logFC, y = .data$logadjp, linetype = .data$line),
colour="darkgrey",
size=0.6,
linewidth=0.6,
show.legend=TRUE) +
scale_linetype_manual(values=c('twodash'=6),
labels=c(paste0("Adj p-value cutoff (", sig, ")"))
Expand Down Expand Up @@ -622,19 +622,19 @@
## three lines, with order color first and then assign linetype manual
pfinal = ptemp +
geom_line(data=sigcut,
aes_string(x='logFC', y='logadjp', linetype='line'),
aes(x = .data$logFC, y = .data$logadjp, linetype = .data$line),
colour="darkgrey",
size=0.6,
linewidth=0.6,
show.legend=TRUE) +
geom_line(data=FCcutpos,
aes_string(x='logFC', y='logadjp', linetype='line'),
aes(x = .data$logFC, y = .data$logadjp, linetype = .data$line),
colour="darkgrey",
size=0.6,
linewidth=0.6,
show.legend=TRUE) +
geom_line(data=FCcutneg,
aes_string(x='logFC', y='logadjp', linetype='line'),
aes(x = .data$logFC, y = .data$logadjp, linetype = .data$line),
colour="darkgrey",
size=0.6) +
linewidth=0.6) +
scale_linetype_manual(values=c('dotted'=3, 'twodash'=6),
labels=c(paste0("Fold change cutoff (", FCcutoff,
")"),
Expand Down Expand Up @@ -671,4 +671,4 @@
if (isPlotly) {
plots
}
}
}
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